From 0ab32333c6bf4951d77b6b69009b4ecf9a24ec5d Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Wed, 28 Oct 2026 10:45:49 +0100 Subject: [PATCH 01/10] Template update for nf-core/tools version 4.2.1 --- .github/actions/get-shards/action.yml | 2 +- .github/actions/nf-test/action.yml | 12 +-- .github/workflows/branch.yml | 2 +- .github/workflows/download_pipeline.yml | 12 +-- .github/workflows/fix-linting.yml | 21 +++++ .github/workflows/fix_linting.yml | 85 ------------------- .github/workflows/linting.yml | 16 ++-- .github/workflows/linting_comment.yml | 28 ------ .github/workflows/nf-test.yml | 6 +- .github/workflows/pr-comment.yml | 2 +- .../workflows/template-version-comment.yml | 2 +- .gitignore | 2 + .nf-core.yml | 5 +- .pre-commit-config.yaml | 2 +- .vscode/extensions.json | 12 +++ .vscode/settings.json | 3 +- README.md | 2 +- conf/base.config | 1 - modules.json | 2 +- nextflow.config | 4 +- nextflow_schema.json | 2 +- nf-test.config | 2 +- ro-crate-metadata.json | 82 +++++++++++------- .../utils_nfcore_lrsomatic_pipeline/main.nf | 4 +- .../nf-core/utils_nfcore_pipeline/meta.yml | 4 +- 25 files changed, 128 insertions(+), 187 deletions(-) create mode 100644 .github/workflows/fix-linting.yml delete mode 100644 .github/workflows/fix_linting.yml delete mode 100644 .github/workflows/linting_comment.yml create mode 100644 .vscode/extensions.json diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml index e2833ee9..2f6859ce 100644 --- a/.github/actions/get-shards/action.yml +++ b/.github/actions/get-shards/action.yml @@ -21,7 +21,7 @@ runs: using: "composite" steps: - name: Install nf-test - uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 + uses: nf-core/setup-nf-test@v2 with: version: ${{ env.NFT_VER }} - name: Get number of shards diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 4175e3c8..ba7095e8 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -20,24 +20,24 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 + uses: nf-core/setup-nextflow@v3 with: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 + uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7 with: - python-version: "3.14" + python-version: "3.15" - name: Install nf-test - uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 + uses: nf-core/setup-nf-test@v2 with: version: "${{ env.NFT_VER }}" install-pdiff: true - name: Setup apptainer if: contains(inputs.profile, 'singularity') - uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0 + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2 - name: Set up Singularity if: contains(inputs.profile, 'singularity') @@ -48,7 +48,7 @@ runs: - name: Conda setup if: contains(inputs.profile, 'conda') - uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4 + uses: conda-incubator/setup-miniconda@be893c923ea9cf1cf7cd510fbdde27c7e18cbdcb # v4.1.0 with: auto-update-conda: true conda-solver: libmamba diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 7626b4a5..8414993e 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -56,7 +56,7 @@ jobs: - name: Upload PR comment artifact if: failure() - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: pr-comment path: pr-comment/ diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index ca2eb822..8d2d4f7c 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -42,18 +42,18 @@ jobs: uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 + uses: nf-core/setup-nextflow@v3 - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + uses: jlumbroso/free-disk-space@ceedf095f4ec1a097402bc6bd80831f2e1a6fde6 # v2.0.0 - - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 + - uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7 with: - python-version: "3.14" + python-version: "3.15" architecture: "x64" - name: Setup Apptainer - uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2 with: apptainer-version: 1.3.4 @@ -135,7 +135,7 @@ jobs: fi - name: Upload Nextflow logfile for debugging purposes - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: nextflow_logfile.txt path: .nextflow.log* diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml new file mode 100644 index 00000000..81ac1812 --- /dev/null +++ b/.github/workflows/fix-linting.yml @@ -0,0 +1,21 @@ +name: Fix linting from a comment +on: + issue_comment: + types: [created] # Add "@nf-core-bot fix linting" as a PR comment to trigger this workflow. + +concurrency: + group: ${{ github.workflow }}-${{ github.event.issue.number }} + +jobs: + fix-linting: + uses: nf-core/actions/.github/workflows/fix-linting.yml@v1 + with: + nextflow-versions: '["25.10.4","latest-everything"]' + permissions: + actions: read + contents: read + issues: write + pull-requests: write + + secrets: + BOT_TOKEN: ${{ secrets.nf_core_bot_auth_token }} diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml deleted file mode 100644 index 61394953..00000000 --- a/.github/workflows/fix_linting.yml +++ /dev/null @@ -1,85 +0,0 @@ -name: Fix linting from a comment -on: - issue_comment: - types: [created] - -jobs: - fix-linting: - # Only run if comment is on a PR with the main repo, and if it contains the magic keywords - if: > - contains(github.event.comment.html_url, '/pull/') && - contains(github.event.comment.body, '@nf-core-bot fix linting') && - github.repository == 'IntGenomicsLab/lrsomatic' - runs-on: ubuntu-latest - steps: - # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - with: - token: ${{ secrets.nf_core_bot_auth_token }} - - # indication that the linting is being fixed - - name: React on comment - uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 - with: - comment-id: ${{ github.event.comment.id }} - reactions: eyes - - # Action runs on the issue comment, so we don't get the PR by default - # Use the gh cli to check out the PR - - name: Checkout Pull Request - run: gh pr checkout ${{ github.event.issue.number }} - env: - GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - - name: Install Nextflow - uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - # Install and run prek - - name: Run prek - id: prek - uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 - continue-on-error: true - - # indication that the linting has finished - - name: react if linting finished succesfully - if: steps.prek.outcome == 'success' - uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 - with: - comment-id: ${{ github.event.comment.id }} - reactions: "+1" - - - name: Commit & push changes - id: commit-and-push - if: steps.prek.outcome == 'failure' - run: | - git config user.email "core@nf-co.re" - git config user.name "nf-core-bot" - git config push.default upstream - git add . - git status - git commit -m "[automated] Fix code linting" - git push - - - name: react if linting errors were fixed - id: react-if-fixed - if: steps.commit-and-push.outcome == 'success' - uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 - with: - comment-id: ${{ github.event.comment.id }} - reactions: hooray - - - name: react if linting errors were not fixed - if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 - with: - comment-id: ${{ github.event.comment.id }} - reactions: confused - - - name: react if linting errors were not fixed - if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 - with: - issue-number: ${{ github.event.issue.number }} - body: | - @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. - See [CI log](https://github.com/IntGenomicsLab/lrsomatic/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 277f12fb..7811abe5 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 + uses: nf-core/setup-nextflow@v3 - name: Run prek - uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 + uses: j178/prek-action@44924fe9ef4a6f88253c4b6b1bf11c689d3ce53d # v3.1.0 nf-core: runs-on: ubuntu-latest @@ -26,15 +26,15 @@ jobs: uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 + uses: nf-core/setup-nextflow@v3 - - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 + - uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7 with: - python-version: "3.14" + python-version: "3.15" architecture: "x64" - name: Setup uv - uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + uses: astral-sh/setup-uv@07a047e608db84b3d8c06cd9a7c7dcc9c355c18e # v10.3.2 - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 @@ -67,7 +67,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: linting-logs path: | @@ -88,7 +88,7 @@ jobs: - name: Upload PR comment artifact if: ${{ always() }} - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: pr-comment path: pr-comment/ diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml deleted file mode 100644 index 5b0c24f7..00000000 --- a/.github/workflows/linting_comment.yml +++ /dev/null @@ -1,28 +0,0 @@ -name: nf-core linting comment -# This workflow is triggered after the linting action is complete -# It posts an automated comment to the PR, even if the PR is coming from a fork - -on: - workflow_run: - workflows: ["nf-core linting"] - -jobs: - test: - runs-on: ubuntu-latest - steps: - - name: Download lint results - uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 - with: - workflow: linting.yml - workflow_conclusion: completed - - - name: Get PR number - id: pr_number - run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - - - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3 - with: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - number: ${{ steps.pr_number.outputs.pr_number }} - path: linting-logs/lint_results.md diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 3dc798a8..f40928a7 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -125,7 +125,7 @@ jobs: - name: Upload PR comment fragment if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7 with: name: pr-comment-fragment-${{ strategy.job-index }} path: pr-comment-fragment/ @@ -158,7 +158,7 @@ jobs: - name: Download PR comment fragments if: ${{ always() }} - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 continue-on-error: true with: pattern: pr-comment-fragment-* @@ -192,7 +192,7 @@ jobs: - name: Upload PR comment artifact if: ${{ always() }} - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7 with: name: pr-comment path: pr-comment/ diff --git a/.github/workflows/pr-comment.yml b/.github/workflows/pr-comment.yml index ab7b59dd..093fa638 100644 --- a/.github/workflows/pr-comment.yml +++ b/.github/workflows/pr-comment.yml @@ -31,7 +31,7 @@ jobs: if: github.event.workflow_run.event == 'pull_request' steps: - name: Download PR comment artifact - uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 + uses: dawidd6/action-download-artifact@eab87c9830c39eff17e5a6eadb20bfb4bc880477 # v27 with: run_id: ${{ github.event.workflow_run.id }} name: pr-comment diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index 149e2851..775758ba 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -54,7 +54,7 @@ jobs: fi - name: Upload PR comment artifact - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: pr-comment path: pr-comment/ diff --git a/.gitignore b/.gitignore index cc2b1a77..b55a302b 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,5 @@ testing* *.pyc null/ .lineage/ +.nf-test/ +.nf-test.log diff --git a/.nf-core.yml b/.nf-core.yml index 0caf039c..440f539f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -19,7 +19,6 @@ lint: - assets/email_template.txt - docs/README.md - .github/workflows/branch.yml - - .github/workflows/linting_comment.yml - .github/workflows/linting.yml multiqc_config: - report_comment @@ -30,7 +29,9 @@ lint: - validation.help.afterText - validation.summary.beforeText - validation.summary.afterText -nf_core_version: 4.1.0 + nf_test_content: + - tests/sv_annotation_compose.nf.test +nf_core_version: 4.2.1 repository_type: pipeline template: author: Robert Forsyth & Luuk Harbers diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e9503db1..4e795210 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.9.6 + - prettier@3.9.10 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: diff --git a/.vscode/extensions.json b/.vscode/extensions.json new file mode 100644 index 00000000..8389b2db --- /dev/null +++ b/.vscode/extensions.json @@ -0,0 +1,12 @@ +{ + // See https://github.com/nf-core/vscode-extensionpack + "recommendations": [ + "codezombiech.gitignore", + "esbenp.prettier-vscode", + "jebbs.markdown-extended", + "mechatroner.rainbow-csv", + "nextflow.nextflow", + "onnovalkering.vscode-singularity", + "redhat.vscode-yaml" + ] +} diff --git a/.vscode/settings.json b/.vscode/settings.json index a33b527c..a0033586 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,3 +1,4 @@ { - "markdown.styles": ["public/vscode_markdown.css"] + // Render nf-core website admonitions nicely in markdown previews + "markdown.styles": ["https://nf-co.re/vscode_markdown.css"] } diff --git a/README.md b/README.md index edd145d8..c44f7f15 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.2.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.2.1) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/conf/base.config b/conf/base.config index 40eeb06a..6da3655c 100644 --- a/conf/base.config +++ b/conf/base.config @@ -63,7 +63,6 @@ process { maxRetries = 2 } withLabel: process_gpu { - ext.use_gpu = { workflow.profile.contains('gpu') } accelerator = { workflow.profile.contains('gpu') ? 1 : null } } } diff --git a/modules.json b/modules.json index 94325c4f..9d29e713 100644 --- a/modules.json +++ b/modules.json @@ -21,7 +21,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8", + "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/nextflow.config b/nextflow.config index 7dea9172..af3eaaec 100644 --- a/nextflow.config +++ b/nextflow.config @@ -257,11 +257,13 @@ manifest { nextflowVersion = '!>=25.10.4' version = '1.1.0' doi = '' + // TODO nf-core: Make a metro map and add relative path to the SVG below. See https://nf-co.re/docs/community/brand/workflow-schematics + // diagram = 'docs/images/metro_map.svg' } // Nextflow plugins plugins { - id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.7.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/nextflow_schema.json b/nextflow_schema.json index 64df1c2d..087357d0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -213,7 +213,7 @@ }, "trace_report_suffix": { "type": "string", - "fa_icon": "far calendar", + "fa_icon": "far fa-calendar", "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", "hidden": true }, diff --git a/nf-test.config b/nf-test.config index f7aaeb4a..7d48da1a 100644 --- a/nf-test.config +++ b/nf-test.config @@ -33,6 +33,6 @@ config { // load the necessary plugins plugins { - load "nft-utils@0.0.3" + load "nft-utils@1.2.1" } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index c34b41cd..2d148b99 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -1,29 +1,23 @@ { "@context": [ - "https://w3id.org/ro/crate/1.2/context", - { - "GithubService": "https://w3id.org/ro/terms/test#GithubService", - "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", - "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine", - "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition", - "TestInstance": "https://w3id.org/ro/terms/test#TestInstance", - "TestService": "https://w3id.org/ro/terms/test#TestService", - "TestSuite": "https://w3id.org/ro/terms/test#TestSuite", - "TravisService": "https://w3id.org/ro/terms/test#TravisService", - "definition": "https://w3id.org/ro/terms/test#definition", - "engineVersion": "https://w3id.org/ro/terms/test#engineVersion", - "instance": "https://w3id.org/ro/terms/test#instance", - "resource": "https://w3id.org/ro/terms/test#resource", - "runsOn": "https://w3id.org/ro/terms/test#runsOn" - } + "https://w3id.org/ro/crate/1.3/context", + "https://w3id.org/ro/terms/test" ], "@graph": [ { "@id": "./", "@type": "Dataset", + "conformsTo": [ + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.1" + }, + { + "@id": "https://w3id.org/ro/wftest/0.2" + } + ], "creativeWorkStatus": "Stable", - "datePublished": "2026-08-14T13:33:32+00:00", - "description": "# IntGenomicsLab/lrsomatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lrsomatic was originally written by Robert Forsyth & Luuk Harbers.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-10-28T09:45:28+00:00", + "description": "# IntGenomicsLab/lrsomatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.2.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.2.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lrsomatic was originally written by Robert Forsyth & Luuk Harbers.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -93,7 +87,7 @@ }, "mentions": [ { - "@id": "#ded8aa2d-e051-4884-94b1-3be4483d2ca4" + "@id": "#da1673e9-7cfa-4bd8-85b8-23964dc96527" } ], "name": "IntGenomicsLab/lrsomatic" @@ -104,14 +98,9 @@ "about": { "@id": "./" }, - "conformsTo": [ - { - "@id": "https://w3id.org/ro/crate/1.2" - }, - { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" - } - ] + "conformsTo": { + "@id": "https://w3id.org/ro/crate/1.3" + } }, { "@id": "main.nf", @@ -120,8 +109,13 @@ "SoftwareSourceCode", "ComputationalWorkflow" ], + "contributor": [ + { + "@id": "#82abb23d-c07a-4f6a-851f-3a9befcbec2b" + } + ], "dateCreated": "", - "dateModified": "2026-08-14T15:33:32Z", + "dateModified": "2026-10-28T10:45:28Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -141,10 +135,9 @@ }, "url": [ "https://github.com/IntGenomicsLab/lrsomatic", - "https://nf-co.re/IntGenomicsLab/lrsomatic//" + "https://nf-co.re/IntGenomicsLab/lrsomatic/1.1.0/" ], "version": [ - "", "1.1.0" ] }, @@ -161,11 +154,20 @@ "version": "!>=25.10.4" }, { - "@id": "#ded8aa2d-e051-4884-94b1-3be4483d2ca4", + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.1", + "@type": [ + "CreativeWork", + "Profile" + ], + "name": "Workflow RO-Crate", + "version": "1.1" + }, + { + "@id": "#da1673e9-7cfa-4bd8-85b8-23964dc96527", "@type": "TestSuite", "instance": [ { - "@id": "#0a084c28-c353-4696-acfc-3e7c84fdf983" + "@id": "#9aaa2407-84bb-44b7-86b9-9e70e5837e79" } ], "mainEntity": { @@ -174,7 +176,16 @@ "name": "Test suite for IntGenomicsLab/lrsomatic" }, { - "@id": "#0a084c28-c353-4696-acfc-3e7c84fdf983", + "@id": "https://w3id.org/ro/wftest/0.2", + "@type": [ + "CreativeWork", + "Profile" + ], + "name": "Workflow Testing RO-Crate", + "version": "0.2" + }, + { + "@id": "#9aaa2407-84bb-44b7-86b9-9e70e5837e79", "@type": "TestInstance", "name": "GitHub Actions workflow for testing IntGenomicsLab/lrsomatic", "resource": "repos/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml", @@ -291,6 +302,11 @@ "@type": "Organization", "name": "nf-core", "url": "https://nf-co.re/" + }, + { + "@id": "#82abb23d-c07a-4f6a-851f-3a9befcbec2b", + "@type": "Person", + "name": "Robert Forsyth & Luuk Harbers" } ] } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index 87df1bdf..2799cadb 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -72,7 +72,7 @@ workflow PIPELINE_INITIALISATION { before_text, after_text, command, - false + null ) // @@ -148,7 +148,7 @@ workflow PIPELINE_COMPLETION { plaintext_email, outdir, monochrome_logs, - multiqc_reports.getVal(), + multiqc_reports.isBound() ? multiqc_reports.getVal() : [], ) } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml index d08d2434..a32b454d 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -13,10 +13,10 @@ input: description: | Nextflow CLI positional arguments output: - - success: + - valid_config: type: boolean description: | - Dummy output to indicate success + Whether a custom configuration or profile was provided to the pipeline authors: - "@adamrtalbot" maintainers: From 7c6e9fe720e350597f4b6e60bbbf653de2f6b8dd Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Wed, 28 Oct 2026 11:52:59 +0100 Subject: [PATCH 02/10] Refresh stale extended-test snapshots clair_only, consensus, deep_only and union run only on release or dispatch, so they were last regenerated on 6 Oct and have drifted since: the haplotagged tumour BAM/BAI md5s and Severus breakpoints_double.csv. Not caused by the template update: the same two tests regenerated on unmodified dev (2b1d510) give byte-identical snapshots apart from timestamps. Co-Authored-By: Claude Opus 5.5 --- tests/clair_only.nf.test.snap | 34 +++++++++++++++++----------------- tests/consensus.nf.test.snap | 22 +++++++++++----------- tests/deep_only.nf.test.snap | 22 +++++++++++----------- tests/union.nf.test.snap | 22 +++++++++++----------- 4 files changed, 50 insertions(+), 50 deletions(-) diff --git a/tests/clair_only.nf.test.snap b/tests/clair_only.nf.test.snap index d0518faf..9bff949b 100644 --- a/tests/clair_only.nf.test.snap +++ b/tests/clair_only.nf.test.snap @@ -3,11 +3,11 @@ "content": [ "88c8d3cf9cb49fdbc53372b2275d5f3e" ], + "timestamp": "2026-09-02T10:24:37.511974063", "meta": { "nf-test": "0.9.4", "nextflow": "26.04.3" - }, - "timestamp": "2026-09-02T10:24:37.511974063" + } }, "-profile test, clair only, extended samplesheet": { "content": [ @@ -806,8 +806,8 @@ [ "sample1_normal.bam:md5,9f778338336c41085b8d0f626f4ed3e3", "sample1_normal.bam.bai:md5,51a07b9bb493578602f1db320fd9e778", - "sample1_tumor.bam:md5,8b74c0425ca53674a3f29b27d33f811a", - "sample1_tumor.bam.bai:md5,0e3fce541093eb470c1b0d98f44f120e", + "sample1_tumor.bam:md5,6fb23863ea4a0feb283d5006808c0c3c", + "sample1_tumor.bam.bai:md5,00cc7ab78b8002719f34744ab4760857", "sample1_normal.flagstat:md5,1c41ea9923945501eb7e41f83a90502d", "sample1_normal.idxstats:md5,902e503387799123ea59255e3fca172c", "sample1_normal.stats:md5,d79e3c68505d39cf29641dfdf5849ef1", @@ -819,7 +819,7 @@ "sample1_whatshap_stats.tsv:md5,cf8917be389dfef1344eeb6b7e99c7c5", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,003e4e80ec4233315762233e5f1ec0d8", + "breakpoints_double.csv:md5,e307fa52370d89e72ea09f84d4eff2f7", "read_qual.txt:md5,92321a03aae1168fdce8ea921b635036", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", @@ -838,12 +838,12 @@ "sample2_whatshap_stats.tsv:md5,31f4d9c3228d60ac463695ca19d05f3a", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,ab7ccd32508029426ca1365053fdc23b", + "breakpoints_double.csv:md5,fa0c1072b74d3dcf914901f73154bbad", "read_qual.txt:md5,57aaac5f18f81b1cbde13e49c012651a", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "sample3_tumor.bam:md5,06eb979bcc58aac9dc9429f2c6a91b1c", - "sample3_tumor.bam.bai:md5,59c95f7b5733008f51de5f30bd902ff7", + "sample3_tumor.bam:md5,9983ad703deaadf2765da20f40cfa206", + "sample3_tumor.bam.bai:md5,f18b06f6e424c7e5d418d2235f168c2e", "sample3_tumor.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3_tumor.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3_tumor.stats:md5,9d2945cfd8813c828d702e86afbaa58b", @@ -852,7 +852,7 @@ "sample3_whatshap_stats.tsv:md5,f7cc79156f23e884ead18e50b8434dbf", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,c18b66eebc1714279e685ab1c56d6cf3", + "breakpoints_double.csv:md5,0c3021e35f1e8b0ae78fd2783e678c9f", "read_qual.txt:md5,f6d803b54f3aa4a36f21af1a9a97923f", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", @@ -864,12 +864,12 @@ "sample4_whatshap_stats.tsv:md5,804922ca6ebd94ae71a7a4058fa9e156", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,1b6b52f5a606d329dcf18226dc0babd0", + "breakpoints_double.csv:md5,e5a537ffb30a6fc9f78ea88d3a5596e2", "read_qual.txt:md5,1efaf50beda973a8e6502566a212628c", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "sample5_tumor.bam:md5,79d8899d89e68b1923ed49ac3ffa2746", - "sample5_tumor.bam.bai:md5,c2c90700339fddbd70c6a7198f843b7c", + "sample5_tumor.bam:md5,fcb61ade133e072cd8e7595610d80636", + "sample5_tumor.bam.bai:md5,50fbd04a1801214fa676bd7958dc6a86", "sample5_tumor.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample5_tumor.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample5_tumor.stats:md5,d757137207bc345e962cc3c9640252f2", @@ -878,16 +878,16 @@ "sample5_whatshap_stats.tsv:md5,0ec14e83f9ad788104de1c6ef3f021f2", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,8f023c63deb462ea4b55566babd365d0", + "breakpoints_double.csv:md5,d61891bf2f24f4a94498a953210287a3", "read_qual.txt:md5,f6d803b54f3aa4a36f21af1a9a97923f", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50" ] ], + "timestamp": "2026-10-28T11:10:57.095837215", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-10-05T20:09:59.776226598" + "nf-test": "0.9.4", + "nextflow": "26.04.3" + } } } \ No newline at end of file diff --git a/tests/consensus.nf.test.snap b/tests/consensus.nf.test.snap index 5d0f1fc5..d641c78e 100644 --- a/tests/consensus.nf.test.snap +++ b/tests/consensus.nf.test.snap @@ -679,8 +679,8 @@ [ "sample1_normal.bam:md5,529e96162af6f913be7e50a210365d8a", "sample1_normal.bam.bai:md5,034f8853f7aa7907adb51a16b56a94f9", - "sample1_tumor.bam:md5,fe9c35bc653348f062189cd495ed5208", - "sample1_tumor.bam.bai:md5,cca02afab0659bd5aa8941a331ba87dd", + "sample1_tumor.bam:md5,d1f6cb4bf17eff53d18206ec631e621e", + "sample1_tumor.bam.bai:md5,34665ec29ead4e94ab0d8c0d550a2d6d", "sample1_normal.flagstat:md5,1c41ea9923945501eb7e41f83a90502d", "sample1_normal.idxstats:md5,902e503387799123ea59255e3fca172c", "sample1_normal.stats:md5,d79e3c68505d39cf29641dfdf5849ef1", @@ -692,7 +692,7 @@ "sample1_whatshap_stats.tsv:md5,ec24f50578a481fcda2cea12dcfd1bae", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,003e4e80ec4233315762233e5f1ec0d8", + "breakpoints_double.csv:md5,c76eef6f53a826ba0d1ea3f84d0befc0", "read_qual.txt:md5,92321a03aae1168fdce8ea921b635036", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", @@ -711,12 +711,12 @@ "sample2_whatshap_stats.tsv:md5,1b2e88694c1f14f946543c191e1f75b7", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,ab7ccd32508029426ca1365053fdc23b", + "breakpoints_double.csv:md5,d5d056ce97784eedf461ad798910f9c2", "read_qual.txt:md5,57aaac5f18f81b1cbde13e49c012651a", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "sample3_tumor.bam:md5,06eb979bcc58aac9dc9429f2c6a91b1c", - "sample3_tumor.bam.bai:md5,59c95f7b5733008f51de5f30bd902ff7", + "sample3_tumor.bam:md5,9983ad703deaadf2765da20f40cfa206", + "sample3_tumor.bam.bai:md5,f18b06f6e424c7e5d418d2235f168c2e", "sample3_tumor.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3_tumor.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3_tumor.stats:md5,9d2945cfd8813c828d702e86afbaa58b", @@ -725,16 +725,16 @@ "sample3_whatshap_stats.tsv:md5,f7cc79156f23e884ead18e50b8434dbf", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,c18b66eebc1714279e685ab1c56d6cf3", + "breakpoints_double.csv:md5,0c3021e35f1e8b0ae78fd2783e678c9f", "read_qual.txt:md5,f6d803b54f3aa4a36f21af1a9a97923f", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50" ] ], + "timestamp": "2026-10-28T11:16:25.596223448", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-10-06T11:13:19.254341842" + "nf-test": "0.9.4", + "nextflow": "26.04.3" + } } } \ No newline at end of file diff --git a/tests/deep_only.nf.test.snap b/tests/deep_only.nf.test.snap index c281dd83..4a9f4862 100644 --- a/tests/deep_only.nf.test.snap +++ b/tests/deep_only.nf.test.snap @@ -615,8 +615,8 @@ [ "sample1_normal.bam:md5,bffc2444a70313bb24a6b52189bbb65a", "sample1_normal.bam.bai:md5,c8162096af7955d5550bb01a9a870013", - "sample1_tumor.bam:md5,a04100696156c1d2c66f2b69e1119048", - "sample1_tumor.bam.bai:md5,3cbed78851ca9d34da2cca80a680bd4a", + "sample1_tumor.bam:md5,c4eaa5bdd47baedb922759cd23599dd4", + "sample1_tumor.bam.bai:md5,0e90c40f3f97f137b9f08bf88557f997", "sample1_normal.flagstat:md5,1c41ea9923945501eb7e41f83a90502d", "sample1_normal.idxstats:md5,902e503387799123ea59255e3fca172c", "sample1_normal.stats:md5,d79e3c68505d39cf29641dfdf5849ef1", @@ -628,7 +628,7 @@ "sample1_whatshap_stats.tsv:md5,46666007fed1d295aba347a9e7618e34", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,003e4e80ec4233315762233e5f1ec0d8", + "breakpoints_double.csv:md5,3dcda68bb247950df3ce73812a087863", "read_qual.txt:md5,92321a03aae1168fdce8ea921b635036", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", @@ -647,12 +647,12 @@ "sample2_whatshap_stats.tsv:md5,b887c4013730bdfa6474ba703dd1ca17", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,ab7ccd32508029426ca1365053fdc23b", + "breakpoints_double.csv:md5,d5d056ce97784eedf461ad798910f9c2", "read_qual.txt:md5,57aaac5f18f81b1cbde13e49c012651a", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "sample3_tumor.bam:md5,8a6d2472ecbcb90f849b12ee14bf3a47", - "sample3_tumor.bam.bai:md5,78eefad4ce39c3ae1ef672cf9a8417f5", + "sample3_tumor.bam:md5,6fa1e11f893633c19a12f927a723216b", + "sample3_tumor.bam.bai:md5,330a63a0285d580ad441ddf5ee5e3027", "sample3_tumor.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3_tumor.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3_tumor.stats:md5,9d2945cfd8813c828d702e86afbaa58b", @@ -661,16 +661,16 @@ "sample3_whatshap_stats.tsv:md5,2dad37f19eea1a9cb75a1b07f584a5ed", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,c18b66eebc1714279e685ab1c56d6cf3", + "breakpoints_double.csv:md5,ff3bd14c47b355d44baa2ca094d0e42f", "read_qual.txt:md5,f6d803b54f3aa4a36f21af1a9a97923f", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50" ] ], + "timestamp": "2026-10-28T11:14:03.646069097", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-10-06T11:29:37.927428469" + "nf-test": "0.9.4", + "nextflow": "26.04.3" + } } } \ No newline at end of file diff --git a/tests/union.nf.test.snap b/tests/union.nf.test.snap index 31b9fc86..274fbb7b 100644 --- a/tests/union.nf.test.snap +++ b/tests/union.nf.test.snap @@ -673,8 +673,8 @@ [ "sample1_normal.bam:md5,157917470659ee56879fd5c8570149c3", "sample1_normal.bam.bai:md5,affa80567bd26028f688cb5d3346fa44", - "sample1_tumor.bam:md5,be58d6ef251d2c044b0dfdc5b6f19c89", - "sample1_tumor.bam.bai:md5,84c74bdfe9cf7d9612d967b9aba95a4c", + "sample1_tumor.bam:md5,3f862b1b46ea5e5149fff01596d5e5bf", + "sample1_tumor.bam.bai:md5,a430335bfdbb92524b388bed2ab9cdb7", "sample1_normal.flagstat:md5,1c41ea9923945501eb7e41f83a90502d", "sample1_normal.idxstats:md5,902e503387799123ea59255e3fca172c", "sample1_normal.stats:md5,d79e3c68505d39cf29641dfdf5849ef1", @@ -686,7 +686,7 @@ "sample1_whatshap_stats.tsv:md5,905ca791c9087b1fbcd14794a6af8b5a", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,003e4e80ec4233315762233e5f1ec0d8", + "breakpoints_double.csv:md5,e307fa52370d89e72ea09f84d4eff2f7", "read_qual.txt:md5,92321a03aae1168fdce8ea921b635036", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", @@ -705,12 +705,12 @@ "sample2_whatshap_stats.tsv:md5,138f333a6c09f4f51db218ed430ec26f", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,ab7ccd32508029426ca1365053fdc23b", + "breakpoints_double.csv:md5,fa0c1072b74d3dcf914901f73154bbad", "read_qual.txt:md5,57aaac5f18f81b1cbde13e49c012651a", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "sample3_tumor.bam:md5,8a6d2472ecbcb90f849b12ee14bf3a47", - "sample3_tumor.bam.bai:md5,78eefad4ce39c3ae1ef672cf9a8417f5", + "sample3_tumor.bam:md5,6fa1e11f893633c19a12f927a723216b", + "sample3_tumor.bam.bai:md5,330a63a0285d580ad441ddf5ee5e3027", "sample3_tumor.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3_tumor.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3_tumor.stats:md5,9d2945cfd8813c828d702e86afbaa58b", @@ -719,16 +719,16 @@ "sample3_whatshap_stats.tsv:md5,2dad37f19eea1a9cb75a1b07f584a5ed", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", - "breakpoints_double.csv:md5,c18b66eebc1714279e685ab1c56d6cf3", + "breakpoints_double.csv:md5,ff3bd14c47b355d44baa2ca094d0e42f", "read_qual.txt:md5,f6d803b54f3aa4a36f21af1a9a97923f", "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50" ] ], + "timestamp": "2026-10-28T11:19:48.20272296", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-10-06T11:40:46.910684091" + "nf-test": "0.9.4", + "nextflow": "26.04.3" + } } } \ No newline at end of file From c8db01354c8285edd1dc01948c768d8e4ee83003 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Wed, 28 Oct 2026 11:53:37 +0100 Subject: [PATCH 03/10] Fill in PR number in CHANGELOG entry Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e451bf6..590d5429 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,8 +30,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- [#PR](https://github.com/IntGenomicsLab/lrsomatic/pull/PR) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, adds a commented-out `manifest.diagram` for a future metro map, replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). -- [#PR](https://github.com/IntGenomicsLab/lrsomatic/pull/PR) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). +- [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, adds a commented-out `manifest.diagram` for a future metro map, replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). +- [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). - [#204](https://github.com/IntGenomicsLab/lrsomatic/pull/204) - With `--modkit_phased` set and haplotype DMR running, `5hmC` is appended to `--modified-bases` whenever `--modkit_args` names `5mC` without it, so the published `modkit_pileup/*_{hp1,hp2,combined}.bed.gz` now carry a 5hmC row next to each 5mC row. `modkit dmr pair` rejects bedMethyl rows whose valid coverage includes uncounted (`N_other`) calls, which ONT SUP data calling both 5mC and 5hmC produces under the `--cpg --modified-bases 5mC` default. Runs with `--skip_dmr`, without `--modkit_phased`, or without DMR references keep `--modkit_args` exactly as given (@YannVRB). - [#205](https://github.com/IntGenomicsLab/lrsomatic/pull/205) - Moved the fiber-seq steps into a `FIBERSEQ` subworkflow and the AmpliconArchitect MD5 default into `aaDataRepoMd5()`, because with dev merged the `LRSOMATIC` workflow body exceeded the 65,535-character limit on a compiled string and failed to compile; behaviour is unchanged (@robert-a-forsyth). - [#205](https://github.com/IntGenomicsLab/lrsomatic/pull/205) - `--download_sigprofiler_genome` now defaults to `true`, so a run without `--sigprofiler_genome_dir` installs the SigProfiler genome instead of stopping at launch; a given directory still wins (@robert-a-forsyth). From ed1ddae01353e0cbf74a45ef624790bcc6170edb Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 29 Oct 2026 11:10:41 +0100 Subject: [PATCH 04/10] Point manifest.diagram at the README metro map Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 2 +- nextflow.config | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 590d5429..0cc8011b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, adds a commented-out `manifest.diagram` for a future metro map, replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). +- [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, sets `manifest.diagram` to the existing metro map (`assets/lrsomatic_1.0.png`), replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). - [#204](https://github.com/IntGenomicsLab/lrsomatic/pull/204) - With `--modkit_phased` set and haplotype DMR running, `5hmC` is appended to `--modified-bases` whenever `--modkit_args` names `5mC` without it, so the published `modkit_pileup/*_{hp1,hp2,combined}.bed.gz` now carry a 5hmC row next to each 5mC row. `modkit dmr pair` rejects bedMethyl rows whose valid coverage includes uncounted (`N_other`) calls, which ONT SUP data calling both 5mC and 5hmC produces under the `--cpg --modified-bases 5mC` default. Runs with `--skip_dmr`, without `--modkit_phased`, or without DMR references keep `--modkit_args` exactly as given (@YannVRB). - [#205](https://github.com/IntGenomicsLab/lrsomatic/pull/205) - Moved the fiber-seq steps into a `FIBERSEQ` subworkflow and the AmpliconArchitect MD5 default into `aaDataRepoMd5()`, because with dev merged the `LRSOMATIC` workflow body exceeded the 65,535-character limit on a compiled string and failed to compile; behaviour is unchanged (@robert-a-forsyth). diff --git a/nextflow.config b/nextflow.config index 60072408..24edbd9b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -474,8 +474,7 @@ manifest { nextflowVersion = '!>=25.10.4' version = '1.1.0' doi = '' - // TODO nf-core: Make a metro map and add relative path to the SVG below. See https://nf-co.re/docs/community/brand/workflow-schematics - // diagram = 'docs/images/metro_map.svg' + diagram = 'assets/lrsomatic_1.0.png' } // Nextflow plugins From b38fdc7112e411fcaf22b77e7a7335604e1a291c Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 29 Oct 2026 13:24:37 +0100 Subject: [PATCH 05/10] Clear pipeline-level nf-core lint warnings, bump to 1.2.0dev - manifest.version 1.1.0 -> 1.2.0dev; snapshot version keys follow - move the 13 flat subworkflows/local/*.nf files to /main.nf (includes one level deeper; explicit .nf paths in paired/, tumor_only/ and the tests updated) - skip_modkit moved into skip_options; descriptions for generate_gvcf, autocorrelation, vep_custom, vep_custom_tbi, severus_minsupport and wakhan_chroms - resolve template TODOs: pipeline citation in the methods description, pipeline-specific contribution guidelines, and drop comments whose work was already done - remove lint_log.txt, a lint debug log committed by mistake - RO-Crate regenerated Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 1 + README.md | 3 - assets/methods_description_template.yml | 4 +- conf/base.config | 2 - docs/CONTRIBUTING.md | 6 +- lint_log.txt | 3596 ----------------- modules/local/cramino/meta.yml | 1 - .../matrixgenerator/tests/main.nf.test | 2 +- nextflow.config | 4 +- nextflow_schema.json | 29 +- ro-crate-metadata.json | 20 +- .../{deepsomatic.nf => deepsomatic/main.nf} | 6 +- subworkflows/local/{dmr.nf => dmr/main.nf} | 8 +- .../local/{ecdna.nf => ecdna/main.nf} | 12 +- .../local/{fiberseq.nf => fiberseq/main.nf} | 8 +- .../main.nf} | 4 +- .../local/paired/paired_smallvar_germline.nf | 2 +- .../local/paired/paired_smallvar_somatic.nf | 4 +- .../main.nf} | 36 +- .../main.nf} | 4 +- .../main.nf} | 2 +- .../main.nf} | 14 +- .../main.nf} | 4 +- .../main.nf} | 14 +- .../main.nf} | 6 +- .../main.nf} | 16 +- subworkflows/local/tests/dmr.nf.test | 2 +- subworkflows/local/tests/ecdna.nf.test | 2 +- .../local/tests/padfoot_annotation.nf.test | 2 +- .../local/tests/prepare_aa_data_repo.nf.test | 2 +- .../local/tests/prepare_signatures.nf.test | 2 +- .../local/tests/reconplot_figures.nf.test | 2 +- .../local/tumor_only/tumoronly_smallvar.nf | 6 +- tests/chm13.nf.test.snap | 2 +- tests/clair_only.nf.test.snap | 2 +- tests/consensus.nf.test.snap | 2 +- tests/deep_only.nf.test.snap | 2 +- tests/default.nf.test.snap | 2 +- tests/nextflow.config | 2 - tests/union.nf.test.snap | 2 +- 40 files changed, 122 insertions(+), 3718 deletions(-) delete mode 100644 lint_log.txt rename subworkflows/local/{deepsomatic.nf => deepsomatic/main.nf} (90%) rename subworkflows/local/{dmr.nf => dmr/main.nf} (92%) rename subworkflows/local/{ecdna.nf => ecdna/main.nf} (91%) rename subworkflows/local/{fiberseq.nf => fiberseq/main.nf} (93%) rename subworkflows/local/{padfoot_annotation.nf => padfoot_annotation/main.nf} (94%) rename subworkflows/local/{phasing_haplotyping.nf => phasing_haplotyping/main.nf} (95%) rename subworkflows/local/{prepare_aa_data_repo.nf => prepare_aa_data_repo/main.nf} (92%) rename subworkflows/local/{prepare_annotation.nf => prepare_annotation/main.nf} (96%) rename subworkflows/local/{prepare_reference_files.nf => prepare_reference_files/main.nf} (93%) rename subworkflows/local/{prepare_signatures.nf => prepare_signatures/main.nf} (94%) rename subworkflows/local/{prepare_vep_plugins.nf => prepare_vep_plugins/main.nf} (86%) rename subworkflows/local/{reconplot_figures.nf => reconplot_figures/main.nf} (94%) rename subworkflows/local/{small_variant_consensus.nf => small_variant_consensus/main.nf} (96%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0cc8011b..6cf736d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#PR](https://github.com/IntGenomicsLab/lrsomatic/pull/PR) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` is now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, sets `manifest.diagram` to the existing metro map (`assets/lrsomatic_1.0.png`), replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). - [#204](https://github.com/IntGenomicsLab/lrsomatic/pull/204) - With `--modkit_phased` set and haplotype DMR running, `5hmC` is appended to `--modified-bases` whenever `--modkit_args` names `5mC` without it, so the published `modkit_pileup/*_{hp1,hp2,combined}.bed.gz` now carry a 5hmC row next to each 5mC row. `modkit dmr pair` rejects bedMethyl rows whose valid coverage includes uncounted (`N_other`) calls, which ONT SUP data calling both 5mC and 5hmC produces under the `--cpg --modified-bases 5mC` default. Runs with `--skip_dmr`, without `--modkit_phased`, or without DMR references keep `--modkit_args` exactly as given (@YannVRB). diff --git a/README.md b/README.md index a8387f74..90ec15e0 100644 --- a/README.md +++ b/README.md @@ -72,9 +72,6 @@ c. Somatic SV and CNA functional annotation ([`Padfoot`](https://github.com/Kolm a. Rearrangement and copy-number figures per CN/SV caller pair ([`ReConPlot`](https://github.com/cortes-ciriano-lab/ReConPlot)) - - ## Usage > [!NOTE] diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index fca23d8a..c157bc19 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,16 +3,16 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "IntGenomicsLab/lrsomatic Methods Description" section_href: "https://github.com/IntGenomicsLab/lrsomatic" plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using IntGenomicsLab/lrsomatic v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (GrΓΌning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

+

Data was processed using IntGenomicsLab/lrsomatic v${workflow.manifest.version} ${doi_text} (Forsyth, Harbers et al., 2026), built with the nf-core framework (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (GrΓΌning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}

${tool_citations}

References

    +
  • Forsyth, R. A., Harbers, L., Verhasselt, A., Rocha IraizΓ³s, A.-L., Yang, S., Vande Velde, J., Davies, C., Pillay, N., Lambrechts, L., & Demeulemeester, J. (2026). LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data. bioRxiv 2026.02.26.707772. doi: 10.64898/2026.02.26.707772
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
  • GrΓΌning, B., Dale, R., SjΓΆdin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., KΓΆster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
    • diff --git a/conf/base.config b/conf/base.config index c12468aa..dce76426 100644 --- a/conf/base.config +++ b/conf/base.config @@ -10,7 +10,6 @@ process { - // TODO nf-core: Check the defaults for all processes cpus = { 1 * task.attempt } memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } @@ -24,7 +23,6 @@ process { // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. - // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_gpu_high { accelerator = { (params.use_gpu as boolean) ? 1 : null } diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 8d7bdfe7..97a76586 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -162,4 +162,8 @@ If you update images or graphics, follow the nf-core [style guidelines](https:// ## Pipeline specific contribution guidelines - +- [ ] Before writing a local module, check whether nf-core/modules already has one, and install it with `nf-core modules install`. +- [ ] Keep the `[ meta, data ]` tuple shape across module and subworkflow boundaries, so sample metadata reaches every downstream step. +- [ ] Put local subworkflows in `subworkflows/local//main.nf`. +- [ ] Add a `CHANGELOG.md` entry with the PR number for every user-facing change. +- [ ] Tag fast (stub) tests with `small`: pull-request CI runs only tests with that tag. The extended pipeline tests (`clair_only`, `consensus`, `deep_only`, `union`) run only on release or manual dispatch, so regenerate their snapshots whenever an output changes. diff --git a/lint_log.txt b/lint_log.txt deleted file mode 100644 index 366aea19..00000000 --- a/lint_log.txt +++ /dev/null @@ -1,3596 +0,0 @@ -[2025-11-27 15:47:39,242] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:47:39,244] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/lustre1/project/stg_00096/home/rforsyth/LRSomatic/lrsomatic, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:47:39,250] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:39,251] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:39,252] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:39,252] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:39,252] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:39,254] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:47:39,258] git.cmd [DEBUG ] Popen(['git', 'version'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:39,260] git.cmd [DEBUG ] Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=True) -[2025-11-27 15:47:40,027] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:40,360] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:40,375] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:47:40,376] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:47:40,376] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:47:40,378] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:40,379] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:40,379] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:41,648] nf_core.pipelines.lint_utils [DEBUG ] The following files were modified by prettier: - -modules.json - - -[2025-11-27 15:47:41,651] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:41,651] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:41,652] nf_core.components.lint [DEBUG ] Registry set to quay.io -[2025-11-27 15:47:41,652] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:47:41,653] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:41,705] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:41,724] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:47:41,724] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:47:41,725] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:47:41,727] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:41,727] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:41,728] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,155] nf_core.pipelines.lint_utils [DEBUG ] The following files were modified by prettier: - -modules.json - - -[2025-11-27 15:47:42,157] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,157] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,158] nf_core.components.lint [DEBUG ] Registry set to quay.io -[2025-11-27 15:47:42,160] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,160] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,160] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,162] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,162] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,163] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,163] nf_core.pipelines.lint [INFO ] Testing pipeline: [magenta]. -[2025-11-27 15:47:42,165] nf_core.pipelines.lint [DEBUG ] Running lint test: files_exist -[2025-11-27 15:47:42,167] nf_core.pipelines.lint [DEBUG ] Running lint test: nextflow_config -[2025-11-27 15:47:42,169] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,169] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,170] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,171] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,171] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,171] nf_core.pipelines.schema [DEBUG ] Ignoring parameters from config: ['genomes'] -[2025-11-27 15:47:42,171] nf_core.pipelines.schema [DEBUG ] Ignoring parameters: ['help', 'help_full', 'show_hidden', 'trace_report_suffix', 'genomes'] -[2025-11-27 15:47:42,172] nf_core.pipelines.schema [DEBUG ] JSON file loaded: nextflow_schema.json -[2025-11-27 15:47:42,172] nf_core.pipelines.lint [DEBUG ] Running lint test: nf_test_content -[2025-11-27 15:47:42,173] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,174] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,174] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,175] nf_core.pipelines.lint [DEBUG ] Running lint test: files_unchanged -[2025-11-27 15:47:42,197] nf_core.utils [DEBUG ] Could not find a config file in the directory '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' -[2025-11-27 15:47:42,378] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:47:42,378] nf_core.utils [DEBUG ] Could not find git hash for pipeline: /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic. /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic -[2025-11-27 15:47:42,378] nf_core.utils [DEBUG ] Got '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' as path -[2025-11-27 15:47:42,378] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-2540e072f807b83f582a63138.json -[2025-11-27 15:47:42,379] nf_core.utils [DEBUG ] No conda `environment.yml` file found. -[2025-11-27 15:47:42,382] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): nf-co.re:443 -[2025-11-27 15:47:42,674] urllib3.connectionpool [DEBUG ] https://nf-co.re:443 "GET /pipelines.json HTTP/1.1" 200 None -[2025-11-27 15:47:42,909] nf_core.pipelines.rocrate [DEBUG ] Adding topics: ['nf-core', 'nextflow'] -[2025-11-27 15:47:42,909] nf_core.pipelines.rocrate [DEBUG ] No git repository found. No git contributors will be added as authors. -[2025-11-27 15:47:42,910] nf_core.pipelines.rocrate [INFO ] Saving metadata file to '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' -[2025-11-27 15:47:42,911] nf_core.utils [DEBUG ] Got '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' as path -[2025-11-27 15:47:42,911] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-2540e072f807b83f582a63138.json -[2025-11-27 15:47:42,911] nf_core.utils [DEBUG ] Using config file: /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic/.nf-core.yml -[2025-11-27 15:47:42,914] nf_core.utils [DEBUG ] Got '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' as path -[2025-11-27 15:47:42,914] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-2540e072f807b83f582a63138.json -[2025-11-27 15:47:42,915] nf_core.utils [DEBUG ] Using config file: /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic/.nf-core.yml -[2025-11-27 15:47:43,547] nf_core.pipelines.lint_utils [DEBUG ] prettier.................................................................Passed - -[2025-11-27 15:47:43,550] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_nf_test -[2025-11-27 15:47:43,556] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_awstest -[2025-11-27 15:47:43,556] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_awsfulltest -[2025-11-27 15:47:43,556] nf_core.pipelines.lint [DEBUG ] Running lint test: readme -[2025-11-27 15:47:43,557] nf_core.pipelines.lint [DEBUG ] Running lint test: pipeline_todos -[2025-11-27 15:47:43,708] nf_core.pipelines.lint [DEBUG ] Running lint test: pipeline_if_empty_null -[2025-11-27 15:50:35,955] nf_core.pipelines.lint [DEBUG ] Running lint test: plugin_includes -[2025-11-27 15:50:35,958] nf_core.pipelines.lint [DEBUG ] Running lint test: pipeline_name_conventions -[2025-11-27 15:50:35,959] nf_core.pipelines.lint [DEBUG ] Running lint test: template_strings -[2025-11-27 15:50:36,008] nf_core.pipelines.lint [DEBUG ] Running lint test: schema_lint -[2025-11-27 15:50:36,008] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,009] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,042] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,042] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,043] nf_core.pipelines.lint [DEBUG ] Skipping lint test 'schema_params' -[2025-11-27 15:50:36,043] nf_core.pipelines.lint [DEBUG ] Running lint test: system_exit -[2025-11-27 15:50:36,093] nf_core.pipelines.lint [DEBUG ] Running lint test: schema_description -[2025-11-27 15:50:36,093] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,093] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,094] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,094] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,125] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_schema_validation -[2025-11-27 15:50:36,126] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): www.schemastore.org:443 -[2025-11-27 15:50:36,292] urllib3.connectionpool [DEBUG ] https://www.schemastore.org:443 "GET /github-workflow HTTP/1.1" 200 14042 -[2025-11-27 15:50:36,454] nf_core.pipelines.lint [DEBUG ] Running lint test: merge_markers -[2025-11-27 15:50:36,514] nf_core.pipelines.lint [DEBUG ] Running lint test: modules_json -[2025-11-27 15:50:36,514] nf_core.pipelines.lint [DEBUG ] Running lint test: multiqc_config -[2025-11-27 15:50:36,516] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,516] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,517] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:50:36,517] nf_core.pipelines.lint [DEBUG ] Running lint test: modules_structure -[2025-11-27 15:50:36,520] nf_core.pipelines.lint [DEBUG ] Running lint test: local_component_structure -[2025-11-27 15:50:36,520] nf_core.pipelines.lint [DEBUG ] Running lint test: base_config -[2025-11-27 15:50:36,522] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,522] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,522] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:50:36,522] nf_core.pipelines.lint.configs [DEBUG ] found sections: [] -[2025-11-27 15:50:36,539] nf_core.pipelines.lint.configs [DEBUG ] found nf_files: ['main.nf', 'workflows/lrsomatic.nf', 'subworkflows/local/tumor_normal_happhase.nf', 'subworkflows/local/tumor_only_happhase.nf', 'subworkflows/local/prepare_annotation.nf', 'subworkflows/local/prepare_reference_files.nf', 'subworkflows/nf-core/utils_nfschema_plugin/main.nf', 'subworkflows/nf-core/bam_stats_samtools/main.nf', 'subworkflows/nf-core/utils_nextflow_pipeline/main.nf', 'subworkflows/nf-core/utils_nfcore_pipeline/main.nf', 'subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf', 'modules/nf-core/ascat/main.nf', 'modules/nf-core/mosdepth/main.nf', 'modules/nf-core/multiqc/main.nf', 'modules/nf-core/wget/main.nf', 'modules/nf-core/unzip/main.nf', 'modules/nf-core/untar/main.nf', 'modules/nf-core/severus/main.nf', 'modules/nf-core/minimap2/align/main.nf', 'modules/nf-core/minimap2/index/main.nf', 'modules/nf-core/bcftools/merge/main.nf', 'modules/nf-core/bcftools/sort/main.nf', 'modules/nf-core/bcftools/concat/main.nf', 'modules/nf-core/modkit/pileup/main.nf', 'modules/nf-core/samtools/idxstats/main.nf', 'modules/nf-core/samtools/faidx/main.nf', 'modules/nf-core/samtools/cat/main.nf', 'modules/nf-core/samtools/index/main.nf', 'modules/nf-core/samtools/stats/main.nf', 'modules/nf-core/samtools/flagstat/main.nf', 'modules/nf-core/longphase/haplotag/main.nf', 'modules/nf-core/longphase/phase/main.nf', 'modules/nf-core/ensemblvep/vep/main.nf', 'modules/nf-core/ensemblvep/download/main.nf', 'modules/nf-core/pigz/uncompress/main.nf', 'modules/local/wakhan/main.nf', 'modules/local/clairs/main.nf', 'modules/local/cramino/main.nf', 'modules/local/metaextract/main.nf', 'modules/local/clairsto/main.nf', 'modules/local/vcfsplit/main.nf', 'modules/local/clair3/main.nf', 'modules/local/fibertoolsrs/fire/main.nf', 'modules/local/fibertoolsrs/predictm6a/main.nf', 'modules/local/fibertoolsrs/qc/main.nf', 'modules/local/fibertoolsrs/nucleosomes/main.nf'] -[2025-11-27 15:50:36,539] nf_core.pipelines.lint [DEBUG ] Running lint test: modules_config -[2025-11-27 15:50:36,541] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,541] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,542] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:50:36,542] nf_core.pipelines.lint.configs [DEBUG ] found sections: ['ENSEMBLVEP_DOWNLOAD'] -[2025-11-27 15:50:36,558] nf_core.pipelines.lint.configs [DEBUG ] found nf_files: ['main.nf', 'workflows/lrsomatic.nf', 'subworkflows/local/tumor_normal_happhase.nf', 'subworkflows/local/tumor_only_happhase.nf', 'subworkflows/local/prepare_annotation.nf', 'subworkflows/local/prepare_reference_files.nf', 'subworkflows/nf-core/utils_nfschema_plugin/main.nf', 'subworkflows/nf-core/bam_stats_samtools/main.nf', 'subworkflows/nf-core/utils_nextflow_pipeline/main.nf', 'subworkflows/nf-core/utils_nfcore_pipeline/main.nf', 'subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf', 'modules/nf-core/ascat/main.nf', 'modules/nf-core/mosdepth/main.nf', 'modules/nf-core/multiqc/main.nf', 'modules/nf-core/wget/main.nf', 'modules/nf-core/unzip/main.nf', 'modules/nf-core/untar/main.nf', 'modules/nf-core/severus/main.nf', 'modules/nf-core/minimap2/align/main.nf', 'modules/nf-core/minimap2/index/main.nf', 'modules/nf-core/bcftools/merge/main.nf', 'modules/nf-core/bcftools/sort/main.nf', 'modules/nf-core/bcftools/concat/main.nf', 'modules/nf-core/modkit/pileup/main.nf', 'modules/nf-core/samtools/idxstats/main.nf', 'modules/nf-core/samtools/faidx/main.nf', 'modules/nf-core/samtools/cat/main.nf', 'modules/nf-core/samtools/index/main.nf', 'modules/nf-core/samtools/stats/main.nf', 'modules/nf-core/samtools/flagstat/main.nf', 'modules/nf-core/longphase/haplotag/main.nf', 'modules/nf-core/longphase/phase/main.nf', 'modules/nf-core/ensemblvep/vep/main.nf', 'modules/nf-core/ensemblvep/download/main.nf', 'modules/nf-core/pigz/uncompress/main.nf', 'modules/local/wakhan/main.nf', 'modules/local/clairs/main.nf', 'modules/local/cramino/main.nf', 'modules/local/metaextract/main.nf', 'modules/local/clairsto/main.nf', 'modules/local/vcfsplit/main.nf', 'modules/local/clair3/main.nf', 'modules/local/fibertoolsrs/fire/main.nf', 'modules/local/fibertoolsrs/predictm6a/main.nf', 'modules/local/fibertoolsrs/qc/main.nf', 'modules/local/fibertoolsrs/nucleosomes/main.nf'] -[2025-11-27 15:50:36,559] nf_core.pipelines.lint [DEBUG ] Running lint test: nfcore_yml -[2025-11-27 15:50:36,563] nf_core.pipelines.lint [DEBUG ] Running lint test: rocrate_readme_sync -[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/local/wakhan/main.nf -[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_input': {}}, {'tumor_index': {}}, {'normal_input': {}}, {'normal_index': {}}, {'vcf': {}}, {'breakpoints': {}}], [{'meta2': {}}, {'reference': {}}]] -[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*/*_genes_genome.html") , emit: genes_genome_html - tuple val(meta), path("*/*_genes_genome.pdf") , emit: genes_genome_pdf - tuple val(meta), path("*/*_genome_copynumbers_breakpoints.html") , emit: breakpoints_html - tuple val(meta), path("*/*_genome_copynumbers_breakpoints.pdf") , emit: breakpoints_pdf - tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.html") , emit: breakpoints_subclonal_html - tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.pdf") , emit: breakpoints_subclonal_pdf - tuple val(meta), path("*/*_genome_copynumbers_details.html") , emit: copynumbers_details_html - tuple val(meta), path("*/*_genome_copynumbers_details.pdf") , emit: copynumbers_details_pdf - tuple val(meta), path("*/bed_output/*.bed") , emit: bed_files - tuple val(meta), path("*/variation_plots/*.html") , emit: variation_plots - tuple val(meta), path("*/vcf_output/*_wakhan_cna_*.vcf") , emit: vcf_files - tuple val(meta), path("*_heatmap_ploidy_purity.html") , emit: heatmap_html - tuple val(meta), path("*_heatmap_ploidy_purity.html.pdf") , emit: heatmap_pdf - tuple val(meta), path("*_optimized_peak.html") , emit: optimized_peak_html - tuple val(meta), path("coverage_data/*.csv") , emit: coverage_csv - tuple val(meta), path("coverage_plots/*.html") , emit: coverage_plots_html - tuple val(meta), path("coverage_plots/*.pdf") , emit: coverage_plots_pdf - tuple val(meta), path("phasing_output/*.html") , emit: phasing_html - tuple val(meta), path("phasing_output/*.pdf") , emit: phasing_pdf - tuple val(meta), path("phasing_output/*.rephased.vcf.gz") , emit: rephased_vcf - tuple val(meta), path("phasing_output/*.rephased.vcf.gz.csi") , emit: rephased_vcf_index - tuple val(meta), path("snps_loh_plots/*_genome_snps_ratio_loh.html") , emit: snps_loh_plot, optional: true - tuple val(meta), path("solutions_ranks.tsv") , emit: solutions_ranks - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 24 outputs in modules/local/wakhan/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Outputs: {'genes_genome_html': [[{'meta': {}}, {'*/*_genes_genome.html': {}}]], 'genes_genome_pdf': [[{'meta': {}}, {'*/*_genes_genome.pdf': {}}]], 'breakpoints_html': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints.html': {}}]], 'breakpoints_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints.pdf': {}}]], 'breakpoints_subclonal_html': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints_subclonal.html': {}}]], 'breakpoints_subclonal_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints_subclonal.pdf': {}}]], 'copynumbers_details_html': [[{'meta': {}}, {'*/*_genome_copynumbers_details.html': {}}]], 'copynumbers_details_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_details.pdf': {}}]], 'bed_files': [[{'meta': {}}, {'*/bed_output/*.bed': {}}]], 'variation_plots': [[{'meta': {}}, {'*/variation_plots/*.html': {}}]], 'vcf_files': [[{'meta': {}}, {'*/vcf_output/*_wakhan_cna_*.vcf': {}}]], 'heatmap_html': [[{'meta': {}}, {'*_heatmap_ploidy_purity.html': {}}]], 'heatmap_pdf': [[{'meta': {}}, {'*_heatmap_ploidy_purity.html.pdf': {}}]], 'optimized_peak_html': [[{'meta': {}}, {'*_optimized_peak.html': {}}]], 'coverage_csv': [[{'meta': {}}, {'coverage_data/*.csv': {}}]], 'coverage_plots_html': [[{'meta': {}}, {'coverage_plots/*.html': {}}]], 'coverage_plots_pdf': [[{'meta': {}}, {'coverage_plots/*.pdf': {}}]], 'phasing_html': [[{'meta': {}}, {'phasing_output/*.html': {}}]], 'phasing_pdf': [[{'meta': {}}, {'phasing_output/*.pdf': {}}]], 'rephased_vcf': [[{'meta': {}}, {'phasing_output/*.rephased.vcf.gz': {}}]], 'rephased_vcf_index': [[{'meta': {}}, {'phasing_output/*.rephased.vcf.gz.csi': {}}]], 'snps_loh_plot': [[{'meta': {}}, {'snps_loh_plots/*_genome_snps_ratio_loh.html': {}}]], 'solutions_ranks': [[{'meta': {}}, {'solutions_ranks.tsv': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*/*_genes_genome.html") , emit: genes_genome_html - tuple val(meta), path("*/*_genes_genome.pdf") , emit: genes_genome_pdf - tuple val(meta), path("*/*_genome_copynumbers_breakpoints.html") , emit: breakpoints_html - tuple val(meta), path("*/*_genome_copynumbers_breakpoints.pdf") , emit: breakpoints_pdf - tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.html") , emit: breakpoints_subclonal_html - tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.pdf") , emit: breakpoints_subclonal_pdf - tuple val(meta), path("*/*_genome_copynumbers_details.html") , emit: copynumbers_details_html - tuple val(meta), path("*/*_genome_copynumbers_details.pdf") , emit: copynumbers_details_pdf - tuple val(meta), path("*/bed_output/*.bed") , emit: bed_files - tuple val(meta), path("*/variation_plots/*.html") , emit: variation_plots - tuple val(meta), path("*/vcf_output/*_wakhan_cna_*.vcf") , emit: vcf_files - tuple val(meta), path("*_heatmap_ploidy_purity.html") , emit: heatmap_html - tuple val(meta), path("*_heatmap_ploidy_purity.html.pdf") , emit: heatmap_pdf - tuple val(meta), path("*_optimized_peak.html") , emit: optimized_peak_html - tuple val(meta), path("coverage_data/*.csv") , emit: coverage_csv - tuple val(meta), path("coverage_plots/*.html") , emit: coverage_plots_html - tuple val(meta), path("coverage_plots/*.pdf") , emit: coverage_plots_pdf - tuple val(meta), path("phasing_output/*.html") , emit: phasing_html - tuple val(meta), path("phasing_output/*.pdf") , emit: phasing_pdf - tuple val(meta), path("phasing_output/*.rephased.vcf.gz") , emit: rephased_vcf - tuple val(meta), path("phasing_output/*.rephased.vcf.gz.csi") , emit: rephased_vcf_index - tuple val(meta), path("snps_loh_plots/*_genome_snps_ratio_loh.html") , emit: snps_loh_plot, optional: true - tuple val(meta), path("solutions_ranks.tsv") , emit: solutions_ranks - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/wakhan/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/local/clairs/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_bam': {}}, {'tumor_bai': {}}, {'normal_bam': {}}, {'normal_bai': {}}, {'model': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}]] -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.vcf.gz"), emit: vcfs - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/local/clairs/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcfs': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.vcf.gz"), emit: vcfs - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clairs/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/cramino/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.txt"), emit: txt - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/cramino/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'txt': [[{'meta': {}}, {'*.txt': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.txt"), emit: txt - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/cramino/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/metaextract/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), env(basecall_model), env(kinetics) , emit: meta_ext - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/metaextract/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'meta_ext': [[{'meta': {}}, {'basecall_model': {}}, {'kinetics': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), env(basecall_model), env(kinetics) , emit: meta_ext - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/metaextract/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 7 inputs in modules/local/clairsto/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_bam': {}}, {'tumor_bai': {}}, {'model': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}], {'dbSNP': {}}, {'colors': {}}, {'onekgenomes': {}}, {'gnomad': {}}] -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf - tuple val(meta), path("indel.vcf.gz.tbi"), emit: indel_tbi - tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf - tuple val(meta), path("snv.vcf.gz.tbi"), emit: snv_tbi - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/clairsto/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'indel_vcf': [[{'meta': {}}, {'indel.vcf.gz': {}}]], 'indel_tbi': [[{'meta': {}}, {'indel.vcf.gz.tbi': {}}]], 'snv_vcf': [[{'meta': {}}, {'snv.vcf.gz': {}}]], 'snv_tbi': [[{'meta': {}}, {'snv.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf - tuple val(meta), path("indel.vcf.gz.tbi"), emit: indel_tbi - tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf - tuple val(meta), path("snv.vcf.gz.tbi"), emit: snv_tbi - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clairsto/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/fire/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/fire/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/fire/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/predictm6a/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/predictm6a/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/predictm6a/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/qc/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.txt"), emit: qc_txt - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/qc/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'qc_txt': [[{'meta': {}}, {'*.txt': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.txt"), emit: qc_txt - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/qc/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/nucleosomes/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/nucleosomes/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/nucleosomes/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/vcfsplit/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'snv_vcf': {}}, {'indel_vcf': {}}]] -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*somatic.vcf.gz") , emit: somatic_vcf - tuple val(meta), path("*somatic.vcf.gz.tbi") , emit: somatic_tbi - tuple val(meta), path("*germline.vcf.gz") , emit: germline_vcf - tuple val(meta), path("*germline.vcf.gz.tbi") , emit: germline_tbi - - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/vcfsplit/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Outputs: {'somatic_vcf': [[{'meta': {}}, {'*somatic.vcf.gz': {}}]], 'somatic_tbi': [[{'meta': {}}, {'*somatic.vcf.gz.tbi': {}}]], 'germline_vcf': [[{'meta': {}}, {'*germline.vcf.gz': {}}]], 'germline_tbi': [[{'meta': {}}, {'*germline.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*somatic.vcf.gz") , emit: somatic_vcf - tuple val(meta), path("*somatic.vcf.gz.tbi") , emit: somatic_tbi - tuple val(meta), path("*germline.vcf.gz") , emit: germline_vcf - tuple val(meta), path("*germline.vcf.gz.tbi") , emit: germline_tbi - - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/vcfsplit/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/local/clair3/main.nf -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'model': {}}, {'platform': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}]] -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*merge_output.vcf.gz"), emit: vcf - tuple val(meta), path("*merge_output.vcf.gz.tbi"), emit: tbi - tuple val(meta), path("*phased_merge_output.vcf.gz"), emit: phased_vcf, optional: true - tuple val(meta), path("*phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/clair3/main.nf -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*merge_output.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*merge_output.vcf.gz.tbi': {}}]], 'phased_vcf': [[{'meta': {}}, {'*phased_merge_output.vcf.gz': {}}]], 'phased_tbi': [[{'meta': {}}, {'*phased_merge_output.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*merge_output.vcf.gz"), emit: vcf - tuple val(meta), path("*merge_output.vcf.gz.tbi"), emit: tbi - tuple val(meta), path("*phased_merge_output.vcf.gz"), emit: phased_vcf, optional: true - tuple val(meta), path("*phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clair3/main.nf -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 8 inputs in modules/nf-core/ascat/main.nf -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input_normal': {}}, {'index_normal': {}}, {'input_tumor': {}}, {'index_tumor': {}}], {'genomeVersion': {}}, {'allele_files': {}}, {'loci_files': {}}, {'bed_file': {}}, {'fasta': {}}, {'gc_file': {}}, {'rt_file': {}}] -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs - tuple val(meta), path("*BAF.txt"), emit: bafs - tuple val(meta), path("*cnvs.txt"), emit: cnvs - tuple val(meta), path("*LogR.txt"), emit: logrs - tuple val(meta), path("*metrics.txt"), emit: metrics - tuple val(meta), path("*png"), emit: png - tuple val(meta), path("*pdf"), emit: pdf, optional: true - tuple val(meta), path("*purityploidy.txt"), emit: purityploidy - tuple val(meta), path("*segments.txt"), emit: segments - tuple val(meta), path("*segments_raw.txt"), emit: segments_raw, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 11 outputs in modules/nf-core/ascat/main.nf -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Outputs: {'allelefreqs': [[{'meta': {}}, {'*alleleFrequencies_chr*.txt': {}}]], 'bafs': [[{'meta': {}}, {'*BAF.txt': {}}]], 'cnvs': [[{'meta': {}}, {'*cnvs.txt': {}}]], 'logrs': [[{'meta': {}}, {'*LogR.txt': {}}]], 'metrics': [[{'meta': {}}, {'*metrics.txt': {}}]], 'png': [[{'meta': {}}, {'*png': {}}]], 'pdf': [[{'meta': {}}, {'*pdf': {}}]], 'purityploidy': [[{'meta': {}}, {'*purityploidy.txt': {}}]], 'segments': [[{'meta': {}}, {'*segments.txt': {}}]], 'segments_raw': [[{'meta': {}}, {'*segments_raw.txt': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs - tuple val(meta), path("*BAF.txt"), emit: bafs - tuple val(meta), path("*cnvs.txt"), emit: cnvs - tuple val(meta), path("*LogR.txt"), emit: logrs - tuple val(meta), path("*metrics.txt"), emit: metrics - tuple val(meta), path("*png"), emit: png - tuple val(meta), path("*pdf"), emit: pdf, optional: true - tuple val(meta), path("*purityploidy.txt"), emit: purityploidy - tuple val(meta), path("*segments.txt"), emit: segments - tuple val(meta), path("*segments_raw.txt"), emit: segments_raw, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ascat/main.nf -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,574] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:36,575] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,839] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,851] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:36,851] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:36,852] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:36,852] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,884] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,887] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/ascat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,888] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/ascat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,986] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,056] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/ascat/main.nf -[2025-11-27 15:50:37,056] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/bcftools/concat/main.nf -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcfs': {}}, {'tbi': {}}]] -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}.${extension}") , emit: vcf - tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true - tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/bcftools/concat/main.nf -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'${prefix}.${extension}': {}}]], 'tbi': [[{'meta': {}}, {'${prefix}.${extension}.tbi': {}}]], 'csi': [[{'meta': {}}, {'${prefix}.${extension}.csi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}.${extension}") , emit: vcf - tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true - tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/concat/main.nf -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:37,057] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:37,058] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,092] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,103] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:37,103] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:37,103] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:37,104] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,135] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,138] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/bcftools/concat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,139] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/bcftools/concat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,225] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,309] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:37,310] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,343] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,353] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:37,354] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:37,354] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:37,354] git.cmd [DEBUG ] Popen(['git', 'checkout', 'e753770db613ce014b3c4bc94f6cba443427b726'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,018] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found 4 inputs in modules/nf-core/bcftools/merge/main.nf -[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcfs': {}}, {'tbis': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}], [{'meta4': {}}, {'bed': {}}]] -[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf - tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/bcftools/merge/main.nf -[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.{bcf,vcf}{,.gz}': {}}]], 'index': [[{'meta': {}}, {'*.{csi,tbi}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf - tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/merge/main.nf -[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:38,213] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:38,213] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,275] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,286] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:38,287] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:38,287] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:38,288] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,346] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,350] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/bcftools/merge'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,351] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/bcftools/merge'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,436] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,518] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:38,518] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,566] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,578] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:38,578] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:38,578] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:38,579] git.cmd [DEBUG ] Popen(['git', 'checkout', 'f17049e03697726ace7499d2fe342f892594f6f3'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:42,382] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/bcftools/sort/main.nf -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcf': {}}]] -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/bcftools/sort/main.nf -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.{vcf,vcf.gz,bcf,bcf.gz}': {}}]], 'tbi': [[{'meta': {}}, {'*.tbi': {}}]], 'csi': [[{'meta': {}}, {'*.csi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/sort/main.nf -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:45,573] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:45,574] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,713] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,727] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:45,727] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:45,727] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:45,728] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,865] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,868] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/bcftools/sort'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,869] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/bcftools/sort'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,959] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,043] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/bcftools/sort/main.nf -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/ensemblvep/download/main.nf -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'assembly': {}}, {'species': {}}, {'cache_version': {}}]] -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path(prefix), emit: cache - path "versions.yml", emit: versions - - -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/ensemblvep/download/main.nf -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Outputs: {'cache': [[{'meta': {}}, {'prefix': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path(prefix), emit: cache - path "versions.yml", emit: versions - - -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ensemblvep/download/main.nf -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:46,044] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:46,045] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,151] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,164] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:46,164] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:46,164] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:46,165] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,208] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,212] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/ensemblvep/download'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,213] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/ensemblvep/download'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,324] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,402] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:46,402] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,455] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,467] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:46,467] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:46,467] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:46,468] git.cmd [DEBUG ] Popen(['git', 'checkout', '2fcc53751152a999bfc9c24f75f494b9e5bb338f'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:49,974] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 9 inputs in modules/nf-core/ensemblvep/vep/main.nf -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcf': {}}, {'custom_extra_files': {}}], {'genome': {}}, {'species': {}}, {'cache_version': {}}, {'cache': {}}, [{'meta2': {}}, {'fasta': {}}], {'extra_files': {}}, {'custom_vep': {}}, {'custom_vep_tbi': {}}] -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true - tuple val(meta), path("*.tab.gz"), emit: tab, optional: true - tuple val(meta), path("*.json.gz"), emit: json, optional: true - path "*.html", emit: report, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 6 outputs in modules/nf-core/ensemblvep/vep/main.nf -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'tab': [[{'meta': {}}, {'*.tab.gz': {}}]], 'json': [[{'meta': {}}, {'*.json.gz': {}}]], 'report': [{'*.html': {}}], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true - tuple val(meta), path("*.tab.gz"), emit: tab, optional: true - tuple val(meta), path("*.json.gz"), emit: json, optional: true - path "*.html", emit: report, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ensemblvep/vep/main.nf -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:53,302] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:53,303] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,408] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,420] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:53,420] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:53,420] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:53,421] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,518] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,522] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/ensemblvep/vep'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,523] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/ensemblvep/vep'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,631] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,709] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/ensemblvep/vep/main.nf -[2025-11-27 15:50:53,709] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/longphase/haplotag/main.nf -[2025-11-27 15:50:53,709] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'snps': {}}, {'svs': {}}, {'mods': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}]] -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.{bam,cram}"), emit: bam - tuple val(meta), path("*.log") , emit: log , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/longphase/haplotag/main.nf -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.{bam,cram}': {}}]], 'log': [[{'meta': {}}, {'*.log': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.{bam,cram}"), emit: bam - tuple val(meta), path("*.log") , emit: log , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/longphase/haplotag/main.nf -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:53,710] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:53,711] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,792] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,804] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:53,805] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:53,806] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:53,806] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,874] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,878] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/longphase/haplotag'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,879] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/longphase/haplotag'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,991] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:54,094] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:54,095] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:54,185] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:54,199] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:54,199] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:54,200] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:54,200] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:58,312] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/longphase/phase/main.nf -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'snps': {}}, {'svs': {}}, {'mods': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}]] -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.vcf.gz") , emit: vcf - tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/longphase/phase/main.nf -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.vcf.gz") , emit: vcf - tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/longphase/phase/main.nf -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:02,039] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:02,040] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,408] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,419] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:02,419] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:02,420] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:02,421] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,475] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,478] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/longphase/phase'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,479] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/longphase/phase'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,590] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,695] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/longphase/phase/main.nf -[2025-11-27 15:51:02,695] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:02,696] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,749] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,761] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:02,761] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:02,761] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:02,762] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:05,703] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 6 inputs in modules/nf-core/minimap2/align/main.nf -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'reads': {}}], [{'meta2': {}}, {'reference': {}}], {'bam_format': {}}, {'bam_index_extension': {}}, {'cigar_paf_format': {}}, {'cigar_bam': {}}] -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.paf") , optional: true, emit: paf - tuple val(meta), path("*.bam") , optional: true, emit: bam - tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/minimap2/align/main.nf -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Outputs: {'paf': [[{'meta': {}}, {'*.paf': {}}]], 'bam': [[{'meta': {}}, {'*.bam': {}}]], 'index': [[{'meta': {}}, {'*.bam.${bam_index_extension}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.paf") , optional: true, emit: paf - tuple val(meta), path("*.bam") , optional: true, emit: bam - tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/minimap2/align/main.nf -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:09,496] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:09,497] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,655] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,667] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:09,667] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:09,667] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:09,668] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,808] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,812] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/minimap2/align'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,813] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/minimap2/align'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,901] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:10,040] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/minimap2/align/main.nf -[2025-11-27 15:51:10,041] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:10,041] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:10,141] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:10,153] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:10,153] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:10,154] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:10,154] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:13,177] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/minimap2/index/main.nf -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'fasta': {}}]] -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.mmi"), emit: index - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/minimap2/index/main.nf -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Outputs: {'index': [[{'meta': {}}, {'*.mmi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.mmi"), emit: index - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/minimap2/index/main.nf -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:16,904] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:16,905] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,209] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,221] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:17,221] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:17,222] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:17,222] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,280] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,284] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/minimap2/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,285] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/minimap2/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,372] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,510] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:17,510] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,570] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,582] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:17,583] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:17,583] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:17,583] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:20,761] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:24,622] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/modkit/pileup/main.nf -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}], [{'meta2': {}}, {'fasta': {}}, {'fai': {}}], [{'meta3': {}}, {'bed': {}}]] -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.bed") , emit: bed , optional: true - tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true - tuple val(meta), path("*.log") , emit: log , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/modkit/pileup/main.nf -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bed': [[{'meta': {}}, {'*.bed': {}}]], 'bedgraph': [[{'meta': {}}, {'*.bedgraph': {}}]], 'log': [[{'meta': {}}, {'*.log': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.bed") , emit: bed , optional: true - tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true - tuple val(meta), path("*.log") , emit: log , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/modkit/pileup/main.nf -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:24,623] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:24,624] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:24,815] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:24,826] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:24,827] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:24,827] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:24,828] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:24,997] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,000] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/modkit/pileup'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,002] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/modkit/pileup'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,119] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,234] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:25,235] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,374] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,386] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:25,386] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:25,386] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:25,387] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:28,381] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/mosdepth/main.nf -[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'bed': {}}], [{'meta2': {}}, {'fasta': {}}]] -[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path('*.global.dist.txt') , emit: global_txt - tuple val(meta), path('*.summary.txt') , emit: summary_txt - tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt - tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4 - tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed - tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi - tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed - tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi - tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed - tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi - tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed - tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Found 13 outputs in modules/nf-core/mosdepth/main.nf -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Outputs: {'global_txt': [[{'meta': {}}, {'*.global.dist.txt': {}}]], 'summary_txt': [[{'meta': {}}, {'*.summary.txt': {}}]], 'regions_txt': [[{'meta': {}}, {'*.region.dist.txt': {}}]], 'per_base_d4': [[{'meta': {}}, {'*.per-base.d4': {}}]], 'per_base_bed': [[{'meta': {}}, {'*.per-base.bed.gz': {}}]], 'per_base_csi': [[{'meta': {}}, {'*.per-base.bed.gz.csi': {}}]], 'regions_bed': [[{'meta': {}}, {'*.regions.bed.gz': {}}]], 'regions_csi': [[{'meta': {}}, {'*.regions.bed.gz.csi': {}}]], 'quantized_bed': [[{'meta': {}}, {'*.quantized.bed.gz': {}}]], 'quantized_csi': [[{'meta': {}}, {'*.quantized.bed.gz.csi': {}}]], 'thresholds_bed': [[{'meta': {}}, {'*.thresholds.bed.gz': {}}]], 'thresholds_csi': [[{'meta': {}}, {'*.thresholds.bed.gz.csi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path('*.global.dist.txt') , emit: global_txt - tuple val(meta), path('*.summary.txt') , emit: summary_txt - tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt - tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4 - tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed - tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi - tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed - tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi - tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed - tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi - tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed - tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/mosdepth/main.nf -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:32,190] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:32,191] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,284] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,295] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:32,296] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:32,297] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:32,298] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,363] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,367] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/mosdepth'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,368] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/mosdepth'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,456] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,599] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:32,600] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,663] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,674] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:32,675] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:32,675] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:32,675] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:35,682] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 6 inputs in modules/nf-core/multiqc/main.nf -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Inputs: [{'multiqc_files': {}}, {'multiqc_config': {}}, {'extra_multiqc_config': {}}, {'multiqc_logo': {}}, {'replace_names': {}}, {'sample_names': {}}] -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found output_data: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/multiqc/main.nf -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Outputs: {'report': [{'*multiqc_report.html': {}}], 'data': [{'*_data': {}}], 'plots': [{'*_plots': {}}], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Output data: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/multiqc/main.nf -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:39,445] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:39,446] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,663] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,675] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:39,675] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:39,676] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:39,677] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,806] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,810] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/multiqc'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,811] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/multiqc'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,903] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:40,049] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:40,050] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:40,147] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:40,160] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:40,160] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:40,161] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:40,161] git.cmd [DEBUG ] Popen(['git', 'checkout', 'a4488d3d09244f29fb4606ba4eef85d59dcc6ad8'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:43,079] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,118] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/pigz/uncompress/main.nf -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'zip': {}}]] -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${uncompressed_filename}") , emit: file - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/pigz/uncompress/main.nf -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Outputs: {'file': [[{'meta': {}}, {'${uncompressed_filename}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${uncompressed_filename}") , emit: file - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/pigz/uncompress/main.nf -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:46,119] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:46,120] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,170] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,183] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:46,184] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:46,184] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:46,185] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,235] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,239] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/pigz/uncompress'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,240] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/pigz/uncompress'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,362] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,485] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:46,486] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,557] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,569] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:46,569] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:46,569] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:46,570] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:49,638] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/cat/main.nf -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input_files': {}}]] -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam - tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram - path "versions.yml" , emit: versions - - - -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/samtools/cat/main.nf -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'${prefix}.bam': {}}]], 'cram': [[{'meta': {}}, {'${prefix}.cram': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam - tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram - path "versions.yml" , emit: versions - - - -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/cat/main.nf -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:53,446] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:53,447] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,665] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,676] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:53,676] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:53,677] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:53,678] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,816] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,820] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/cat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,821] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/cat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,937] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:54,075] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:54,076] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:54,183] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:54,194] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:54,195] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:54,195] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:54,195] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:57,097] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/samtools/faidx/main.nf -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'fasta': {}}], [{'meta2': {}}, {'fai': {}}], {'get_sizes': {}}] -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true - tuple val(meta), path ("*.sizes") , emit: sizes, optional: true - tuple val(meta), path ("*.fai") , emit: fai, optional: true - tuple val(meta), path ("*.gzi") , emit: gzi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/nf-core/samtools/faidx/main.nf -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Outputs: {'fa': [[{'meta': {}}, {'*.{fa,fasta}': {}}]], 'sizes': [[{'meta': {}}, {'*.sizes': {}}]], 'fai': [[{'meta': {}}, {'*.fai': {}}]], 'gzi': [[{'meta': {}}, {'*.gzi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true - tuple val(meta), path ("*.sizes") , emit: sizes, optional: true - tuple val(meta), path ("*.fai") , emit: fai, optional: true - tuple val(meta), path ("*.gzi") , emit: gzi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/faidx/main.nf -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:00,645] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:00,646] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:00,838] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:00,851] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:00,851] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:00,851] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:00,852] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,041] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,045] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/faidx'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,046] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/faidx'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,137] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,305] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:01,306] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,372] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,385] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:01,385] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:01,386] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:01,386] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:04,805] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/flagstat/main.nf -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}]] -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.flagstat"), emit: flagstat - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/flagstat/main.nf -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Outputs: {'flagstat': [[{'meta': {}}, {'*.flagstat': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.flagstat"), emit: flagstat - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/flagstat/main.nf -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:08,779] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:08,780] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,027] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,038] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:09,038] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:09,039] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:09,040] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,096] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,100] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/flagstat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,101] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/flagstat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,188] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,355] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:09,356] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,413] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,426] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:09,426] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:09,426] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:09,426] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:12,547] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/idxstats/main.nf -[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}]] -[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.idxstats"), emit: idxstats - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/idxstats/main.nf -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Outputs: {'idxstats': [[{'meta': {}}, {'*.idxstats': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.idxstats"), emit: idxstats - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/idxstats/main.nf -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:16,623] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:16,623] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,766] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,778] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:16,778] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:16,779] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:16,779] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,892] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,896] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/idxstats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,897] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/idxstats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,985] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:17,153] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:17,154] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:17,256] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:17,268] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:17,268] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:17,269] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:17,269] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:20,320] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/index/main.nf -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input': {}}]] -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.bai") , optional:true, emit: bai - tuple val(meta), path("*.csi") , optional:true, emit: csi - tuple val(meta), path("*.crai"), optional:true, emit: crai - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/samtools/index/main.nf -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bai': [[{'meta': {}}, {'*.bai': {}}]], 'csi': [[{'meta': {}}, {'*.csi': {}}]], 'crai': [[{'meta': {}}, {'*.crai': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.bai") , optional:true, emit: bai - tuple val(meta), path("*.csi") , optional:true, emit: csi - tuple val(meta), path("*.crai"), optional:true, emit: crai - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:23,974] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/index/main.nf -[2025-11-27 15:52:23,974] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:23,974] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:23,974] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,244] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,256] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:24,256] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:24,257] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:24,257] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,308] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,312] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,313] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,401] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,568] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:24,569] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,620] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,631] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:24,632] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:24,632] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:24,632] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:27,563] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/samtools/stats/main.nf -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input': {}}, {'input_index': {}}], [{'meta2': {}}, {'fasta': {}}]] -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.stats"), emit: stats - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/stats/main.nf -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Outputs: {'stats': [[{'meta': {}}, {'*.stats': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.stats"), emit: stats - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/stats/main.nf -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:31,361] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:31,362] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,494] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,506] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:31,507] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:31,507] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:31,508] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,610] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,614] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/stats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,615] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/stats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,702] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,878] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/samtools/stats/main.nf -[2025-11-27 15:52:31,878] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:31,879] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,963] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,975] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:31,976] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:31,976] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:31,976] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:34,930] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/severus/main.nf -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'target_input': {}}, {'target_index': {}}, {'control_input': {}}, {'control_index': {}}, {'vcf': {}}, {'tbi': {}}], [{'meta2': {}}, {'bed': {}}, {'pon_path': {}}]] -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("severus.log") , emit: log - tuple val(meta), path("read_qual.txt") , emit: read_qual - tuple val(meta), path("breakpoints_double.csv") , emit: breakpoints_double - tuple val(meta), path("read_alignments") , emit: read_alignments , optional: true - tuple val(meta), path("read_ids.csv") , emit: read_ids , optional: true - tuple val(meta), path("severus_collaped_dup.bed") , emit: collapsed_dup , optional: true - tuple val(meta), path("severus_LOH.bed") , emit: loh , optional: true - tuple val(meta), path("all_SVs/severus_all.vcf.gz") , emit: all_vcf , optional: true - tuple val(meta), path("all_SVs/severus_all.vcf.gz.tbi") , emit: all_tbi , optional: true - tuple val(meta), path("all_SVs/breakpoint_clusters_list.tsv") , emit: all_breakpoints_clusters_list , optional: true - tuple val(meta), path("all_SVs/breakpoint_clusters.tsv") , emit: all_breakpoints_clusters , optional: true - tuple val(meta), path("all_SVs/plots/severus_*.html") , emit: all_plots , optional: true - tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz") , emit: somatic_vcf //, optional: true - tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz.tbi") , emit: somatic_tbi , optional: true - tuple val(meta), path("somatic_SVs/breakpoint_clusters_list.tsv") , emit: somatic_breakpoints_clusters_list, optional: true - tuple val(meta), path("somatic_SVs/breakpoint_clusters.tsv") , emit: somatic_breakpoints_clusters , optional: true - tuple val(meta), path("somatic_SVs/plots/severus_*.html") , emit: somatic_plots , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 18 outputs in modules/nf-core/severus/main.nf -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Outputs: {'log': [[{'meta': {}}, {'severus.log': {}}]], 'read_qual': [[{'meta': {}}, {'read_qual.txt': {}}]], 'breakpoints_double': [[{'meta': {}}, {'breakpoints_double.csv': {}}]], 'read_alignments': [[{'meta': {}}, {'read_alignments': {}}]], 'read_ids': [[{'meta': {}}, {'read_ids.csv': {}}]], 'collapsed_dup': [[{'meta': {}}, {'severus_collaped_dup.bed': {}}]], 'loh': [[{'meta': {}}, {'severus_LOH.bed': {}}]], 'all_vcf': [[{'meta': {}}, {'all_SVs/severus_all.vcf.gz': {}}]], 'all_tbi': [[{'meta': {}}, {'all_SVs/severus_all.vcf.gz.tbi': {}}]], 'all_breakpoints_clusters_list': [[{'meta': {}}, {'all_SVs/breakpoint_clusters_list.tsv': {}}]], 'all_breakpoints_clusters': [[{'meta': {}}, {'all_SVs/breakpoint_clusters.tsv': {}}]], 'all_plots': [[{'meta': {}}, {'all_SVs/plots/severus_*.html': {}}]], 'somatic_vcf': [[{'meta': {}}, {'somatic_SVs/severus_somatic.vcf.gz': {}}]], 'somatic_tbi': [[{'meta': {}}, {'somatic_SVs/severus_somatic.vcf.gz.tbi': {}}]], 'somatic_breakpoints_clusters_list': [[{'meta': {}}, {'somatic_SVs/breakpoint_clusters_list.tsv': {}}]], 'somatic_breakpoints_clusters': [[{'meta': {}}, {'somatic_SVs/breakpoint_clusters.tsv': {}}]], 'somatic_plots': [[{'meta': {}}, {'somatic_SVs/plots/severus_*.html': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("severus.log") , emit: log - tuple val(meta), path("read_qual.txt") , emit: read_qual - tuple val(meta), path("breakpoints_double.csv") , emit: breakpoints_double - tuple val(meta), path("read_alignments") , emit: read_alignments , optional: true - tuple val(meta), path("read_ids.csv") , emit: read_ids , optional: true - tuple val(meta), path("severus_collaped_dup.bed") , emit: collapsed_dup , optional: true - tuple val(meta), path("severus_LOH.bed") , emit: loh , optional: true - tuple val(meta), path("all_SVs/severus_all.vcf.gz") , emit: all_vcf , optional: true - tuple val(meta), path("all_SVs/severus_all.vcf.gz.tbi") , emit: all_tbi , optional: true - tuple val(meta), path("all_SVs/breakpoint_clusters_list.tsv") , emit: all_breakpoints_clusters_list , optional: true - tuple val(meta), path("all_SVs/breakpoint_clusters.tsv") , emit: all_breakpoints_clusters , optional: true - tuple val(meta), path("all_SVs/plots/severus_*.html") , emit: all_plots , optional: true - tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz") , emit: somatic_vcf //, optional: true - tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz.tbi") , emit: somatic_tbi , optional: true - tuple val(meta), path("somatic_SVs/breakpoint_clusters_list.tsv") , emit: somatic_breakpoints_clusters_list, optional: true - tuple val(meta), path("somatic_SVs/breakpoint_clusters.tsv") , emit: somatic_breakpoints_clusters , optional: true - tuple val(meta), path("somatic_SVs/plots/severus_*.html") , emit: somatic_plots , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/severus/main.nf -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:38,674] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:38,674] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:38,880] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:38,892] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:38,892] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:38,893] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:38,893] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,092] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,096] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/severus'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,097] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/severus'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,214] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,367] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/severus/main.nf -[2025-11-27 15:52:39,367] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:39,368] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,435] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,448] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:39,448] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:39,449] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:39,449] git.cmd [DEBUG ] Popen(['git', 'checkout', '81880787133db07d9b4c1febd152c090eb8325dc'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:49,232] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/untar/main.nf -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'archive': {}}]] -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}"), emit: untar - path "versions.yml", emit: versions - - -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/untar/main.nf -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Outputs: {'untar': [[{'meta': {}}, {'${prefix}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}"), emit: untar - path "versions.yml", emit: versions - - -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/untar/main.nf -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:57,845] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:57,845] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,185] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,197] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:58,198] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:58,198] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:58,199] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,243] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,246] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/untar'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,247] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/untar'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,344] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,548] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:58,549] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,620] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,633] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:58,633] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:58,634] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:58,634] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:01,667] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/unzip/main.nf -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'archive': {}}]] -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}/"), emit: unzipped_archive - path "versions.yml" , emit: versions - - -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/unzip/main.nf -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Outputs: {'unzipped_archive': [[{'meta': {}}, {'${prefix}/': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}/"), emit: unzipped_archive - path "versions.yml" , emit: versions - - -[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/unzip/main.nf -[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:53:05,410] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:05,411] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,637] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,649] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:05,649] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:05,649] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:05,650] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,794] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,798] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/unzip'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,799] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/unzip'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,893] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:06,081] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:06,082] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:06,193] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:06,205] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:06,205] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:06,206] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:06,206] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:09,447] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/wget/main.nf -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'url': {}}]] -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}.${suffix}"), emit: outfile - path "versions.yml" , emit: versions - - -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/wget/main.nf -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Outputs: {'outfile': [[{'meta': {}}, {'${prefix}.${suffix}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}.${suffix}"), emit: outfile - path "versions.yml" , emit: versions - - -[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/wget/main.nf -[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:53:13,328] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:13,328] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,447] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,458] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:13,459] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:13,459] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:13,460] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,563] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,567] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/wget'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,568] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/wget'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,684] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,841] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:13,842] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,932] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,943] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:13,944] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:13,944] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:13,944] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:16,975] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:21,106] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:21,107] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:21,393] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:21,417] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:21,418] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:21,418] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:21,420] git.cmd [DEBUG ] Popen(['git', 'checkout', '05954dab2ff481bcb999f24455da29a5828af08d'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:27,600] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,141] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:38,142] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,286] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,298] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:38,298] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:38,298] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:38,299] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,354] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,358] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/bam_stats_samtools'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,372] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,458] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:38,459] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,517] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,528] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:38,529] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:38,529] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:38,530] git.cmd [DEBUG ] Popen(['git', 'checkout', 'c2b22d85f30a706a3073387f30380704fcae013b'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:51,273] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:04,283] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:54:04,285] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,104] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,146] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:54:05,149] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:54:05,150] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:54:05,154] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,466] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,484] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/utils_nextflow_pipeline'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,611] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,766] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:54:05,768] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,968] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:06,009] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:54:06,011] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:54:06,012] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:54:06,013] git.cmd [DEBUG ] Popen(['git', 'checkout', '51ae5406a030d4da1e49e4dab49756844fdd6c7a'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:43,965] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:57,578] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:54:57,578] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:57,881] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:57,895] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:54:57,895] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:54:57,896] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:54:57,897] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,070] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,074] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/utils_nfcore_pipeline'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,084] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,172] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:54:58,173] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,226] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,240] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:54:58,241] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:54:58,241] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:54:58,241] git.cmd [DEBUG ] Popen(['git', 'checkout', '2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:06,742] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,344] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:55:16,344] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,558] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,572] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:55:16,573] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:55:16,573] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:55:16,574] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,711] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,716] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/utils_nfschema_plugin'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,727] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,820] nf_core.pipelines.lint [DEBUG ] Printing final results -[2025-11-27 15:55:16,821] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,836] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,836] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,836] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,947] nf_core.components.lint [DEBUG ] Printing final results -[2025-11-27 15:55:16,948] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,960] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,960] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,960] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,960] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,968] nf_core.components.lint [DEBUG ] Printing final results -[2025-11-27 15:55:16,969] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False 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] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,991] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,991] markdown_it.rules_block.fence [DEBUG ] entering fence: 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-[2025-11-27 15:55:16,991] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,992] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False diff --git a/modules/local/cramino/meta.yml b/modules/local/cramino/meta.yml index 93fbea6c..2c2fd2d7 100644 --- a/modules/local/cramino/meta.yml +++ b/modules/local/cramino/meta.yml @@ -1,7 +1,6 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "cramino" -## TODO nf-core: Add a description of the module and list keywords description: A tool for quick quality assessment of cram and bam files, intended for long read sequencing. keywords: - quality diff --git a/modules/local/sigprofiler/matrixgenerator/tests/main.nf.test b/modules/local/sigprofiler/matrixgenerator/tests/main.nf.test index 564d3230..87daee4b 100644 --- a/modules/local/sigprofiler/matrixgenerator/tests/main.nf.test +++ b/modules/local/sigprofiler/matrixgenerator/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_process { setup { run("PREPARE_SIGNATURES") { - script "../../../../../subworkflows/local/prepare_signatures.nf" + script "../../../../../subworkflows/local/prepare_signatures/main.nf" workflow { """ input[0] = 'CHM13-T2T' diff --git a/nextflow.config b/nextflow.config index 24edbd9b..adc6b318 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,7 +9,6 @@ // Global default params, used in configs params { - // TODO nf-core: Specify your pipeline's command line flags // Input options input = null @@ -401,7 +400,6 @@ dag { manifest { name = 'IntGenomicsLab/lrsomatic' contributors = [ - // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ name: 'Luuk Harbers', affiliation: 'VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium', @@ -472,7 +470,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'main' nextflowVersion = '!>=25.10.4' - version = '1.1.0' + version = '1.2.0dev' doi = '' diagram = 'assets/lrsomatic_1.0.png' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 04f31ded..893a4690 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -111,7 +111,8 @@ "fa_icon": "fas fa-filter" }, "generate_gvcf": { - "type": "boolean" + "type": "boolean", + "description": "Also write gVCFs from DeepVariant and DeepSomatic, and publish them next to the VCFs." } } }, @@ -224,7 +225,8 @@ "default": "", "properties": { "autocorrelation": { - "type": "string" + "type": "string", + "description": "Pass --acf to fibertools qc to add the nucleosome autocorrelation to the Fiber-seq QC output. Any non-empty value turns it on." } } }, @@ -259,10 +261,12 @@ "description": "Download the VEP cache if not already present" }, "vep_custom": { - "type": "string" + "type": "string", + "description": "Path to a bgzipped VCF (.vcf.gz) of custom variants for VEP to annotate against. Needs a matching --custom file=... entry in --vep_args." }, "vep_custom_tbi": { - "type": "string" + "type": "string", + "description": "Path to the tabix index of --vep_custom." }, "vep_alphamissense": { "type": "string", @@ -384,7 +388,8 @@ "properties": { "severus_minsupport": { "type": "integer", - "default": 3 + "default": 3, + "description": "Minimum number of supporting reads for Severus to report an SV (Severus --min-support)." }, "severus_whitelist": { "type": "string", @@ -584,7 +589,8 @@ "default": "", "properties": { "wakhan_chroms": { - "type": "string" + "type": "string", + "description": "Comma-separated contigs, or ranges such as chr1-22,chrX, for Wakhan to use. Defaults to chr1-22,chrX for female samples and chr1-22,chrX,chrY for male samples." } } }, @@ -675,6 +681,10 @@ "type": "boolean", "description": "Skips wakhan" }, + "skip_modkit": { + "type": "boolean", + "description": "Skip the modkit pileup of base modifications." + }, "skip_fiber": { "type": "boolean", "description": "Skip Fibertools steps" @@ -1039,10 +1049,5 @@ { "$ref": "#/$defs/generic_options" } - ], - "properties": { - "skip_modkit": { - "type": "boolean" - } - } + ] } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 47ba8849..55848112 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -15,9 +15,9 @@ "@id": "https://w3id.org/ro/wftest/0.2" } ], - "creativeWorkStatus": "Stable", - "datePublished": "2026-10-28T09:47:28+00:00", - "description": "# IntGenomicsLab/lrsomatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.2.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.2.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a robust bioinformatics pipeline designed for processing and analyzing **somatic DNA sequencing** data for long-read sequencing technologies from **Oxford Nanopore** and **PacBio**. It supports both canonical base DNA and modified base calling, including specialized applications such as **Fiber-seq**.\n\nThis **end-to-end pipeline** handles the entire workflow β€” **from raw read processing and alignment, to comprehensive somatic variant calling**, including single nucleotide variants, indels, structural variants, copy number alterations, and modified bases.\n\nIt can be run in both **matched tumour-normal** and **tumour-only mode**, offering flexibility depending on the users study design.\n\nDeveloped using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.\n\nFor more information on how to run the pipeline, you can also go [here](https://intgenomicslab.github.io/lrsomatic).\n\n## Pipeline summary\n\n![image](./assets/lrsomatic_1.0.png)\n\n**1) Pre-processing:**\n\na. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))\n\nb. Alignment to the reference genome ([`minimap2`](https://github.com/lh3/minimap2))\n\nc. Post alignment QC ([`cramino`](https://github.com/wdecoster/cramino), [`samtools idxstats`](https://github.com/samtools/samtools), [`samtools flagstats`](https://github.com/samtools/samtools), [`samtools stats`](https://github.com/samtools/samtools))\n\nd. Specific for calling modified base calling ([`Modkit`](https://github.com/nanoporetech/modkit), [`Fibertools`](https://github.com/fiberseq/fibertools-rs))\n\n**2i) Matched mode: small variant calling:**\n\na. Calling Germline SNPs ([`Clair3`](https://github.com/HKU-BAL/Clair3))\n\nb. Phasing and Haplotagging the SNPs in the normal and tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\nc. Calling somatic SNVs ([`ClairS`](https://github.com/HKU-BAL/ClairS))\n\n**2ii) Tumour only mode: small variant calling:**\n\na. Calling Germline SNPs and somatic SNVs ([`ClairS-TO`](https://github.com/HKU-BAL/ClairS-TO))\n\nb. Phasing and Haplotagging germline SNPs in tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\n**3) Large variant calling:**\n\na. Somatic structural variant calling ([`Severus`](https://github.com/KolmogorovLab/Severus))\n\nb. Somatic structural variant and copy-number calling ([`SAVANA`](https://github.com/cortes-ciriano-lab/savana))\n\nc. Copy number alterion calling; long read version of ([`ASCAT`](https://github.com/VanLoo-lab/ascat))\n\n**4) Annotation:**\n\na. Small variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep)), with pathogenicity and clinical-significance plugins: [`AlphaMissense`](https://github.com/google-deepmind/alphamissense), [`ClinVar`](https://www.ncbi.nlm.nih.gov/clinvar/), [`REVEL`](https://sites.google.com/site/revelgenomics/), [`SIFT`/`PolyPhen`](https://github.com/Ensembl/VEP_plugins), and optionally [`CADD`](https://cadd.gs.washington.edu/) and [`EVE`](https://evemodel.org/)\n\nb. Structural variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\nc. Somatic SV and CNA functional annotation ([`Padfoot`](https://github.com/KolmogorovLab/Padfoot))\n\n**5) Visualisation:**\n\na. Rearrangement and copy-number figures per CN/SV caller pair ([`ReConPlot`](https://github.com/cortes-ciriano-lab/ReConPlot))\n\n\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst prepare a samplesheet with your input data that looks as follows:\n\n```csv\nsample,bam_tumor,bam_normal,platform,sex,fiber\nsample1,tumour.bam,normal.bam,ont,female,n\nsample2,tumour.bam,,ont,female,y\nsample3,tumour.bam,,pb,male,n\nsample4,tumour.bam,normal.bam,pb,male,y\n```\n\nEach row is a sample. BAMs must be unaligned, all fields except `bam_normal` are required, and an empty `bam_normal` runs the sample in tumour-only mode. `platform` is `ont` or `pb`, `sex` is `female` or `male`, and `fiber` is `y` or `n` for Fiber-seq; see the [usage documentation](/docs/usage.md#full-description-of-samplesheet-columns).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\nMore detail is given in our [usage documentation](/docs/usage.md)\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Amber Verhasselt, Alexandra PančíkovΓ‘, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester.\n\n## Pipeline output\n\nThe main output is an aligned and phased tumour BAM, per-sample QC from `cramino`, `mosdepth`, `samtools` and optionally `fibertools`, a MultiQC report, and a self-contained per-sample HTML report (`/report/_report.html`; disable it with `--skip_report`).\n\nVariant and copy number callers (`clairS`, `clairS-TO`, `severus`, `savana`, `ascat`) write to their own folders; Padfoot annotations and ReConPlot figures go to `padfoot/` and `reconplot/`, one subfolder per caller pair. See the [output documentation](/docs/output.md).\n\nExample output directory structure:\n\n```\nβ”œβ”€β”€ Sample 1\nβ”‚ β”œβ”€β”€ ascat\nβ”‚ β”œβ”€β”€ bamfiles\nβ”‚ β”œβ”€β”€ padfoot\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”‚ └── severus_wakhan\nβ”‚ β”œβ”€β”€ qc\nβ”‚ β”‚ β”œβ”€β”€ tumor\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_aln\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_ubam\nβ”‚ β”‚ β”‚ β”œβ”€β”€ fibertoolsrs\nβ”‚ β”‚ β”‚ β”œβ”€β”€ mosdepth\nβ”‚ β”‚ β”‚ β”œβ”€β”€ samtools\nβ”‚ β”œβ”€β”€ reconplot\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”‚ β”œβ”€β”€ severus_ascat\nβ”‚ β”‚ └── severus_wakhan\nβ”‚ β”œβ”€β”€ variants\nβ”‚ β”‚ β”œβ”€β”€clairS-TO\nβ”‚ β”‚ β”œβ”€β”€severus\nβ”‚ β”‚ β”œβ”€β”€savana\nβ”‚ β”œβ”€β”€ vep\nβ”‚ β”‚ β”œβ”€β”€ germline\nβ”‚ β”‚ β”œβ”€β”€ somatic\nβ”‚ β”‚ β”œβ”€β”€ SVs\nβ”‚ β”œβ”€β”€ report\nβ”‚\nβ”œβ”€β”€ Sample 2\nβ”‚ β”œβ”€β”€ ascat\nβ”‚ β”œβ”€β”€ bamfiles\nβ”‚ β”œβ”€β”€ padfoot\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”‚ └── severus_wakhan\nβ”‚ β”œβ”€β”€ qc\nβ”‚ β”‚ β”œβ”€β”€ tumor\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_aln\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_ubam\nβ”‚ β”‚ β”‚ β”œβ”€β”€ fibertoolsrs\nβ”‚ β”‚ β”‚ β”œβ”€β”€ mosdepth\nβ”‚ β”‚ β”‚ β”œβ”€β”€ samtools\nβ”‚ β”‚ β”œβ”€β”€ normal\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_aln\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_ubam\nβ”‚ β”‚ β”‚ β”œβ”€β”€ fibertoolsrs\nβ”‚ β”‚ β”‚ β”œβ”€β”€ mosdepth\nβ”‚ β”‚ β”‚ β”œβ”€β”€ samtools\nβ”‚ β”œβ”€β”€ reconplot\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”‚ β”œβ”€β”€ severus_ascat\nβ”‚ β”‚ └── severus_wakhan\nβ”‚ β”œβ”€β”€ variants\nβ”‚ β”‚ β”œβ”€β”€ clair3\nβ”‚ β”‚ β”œβ”€β”€ clairS\nβ”‚ β”‚ β”œβ”€β”€ severus\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”œβ”€β”€ vep\nβ”‚ β”‚ β”œβ”€β”€ germline\nβ”‚ β”‚ β”œβ”€β”€ somatic\nβ”‚ β”‚ β”œβ”€β”€ SVs\nβ”œβ”€β”€ pipeline_info\n```\n\nmore detail is given in our [output documentation](/docs/output.md)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\nIf you use `IntGenomicsLab/lrsomatic` for your analysis, please cite it using the following:\n\n> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data\n>\n> Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-LucΓ­a Rocha IraizΓ³s, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester\n>\n> bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "creativeWorkStatus": "InProgress", + "datePublished": "2026-10-29T12:23:13+00:00", + "description": "# IntGenomicsLab/lrsomatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.2.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.2.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a robust bioinformatics pipeline designed for processing and analyzing **somatic DNA sequencing** data for long-read sequencing technologies from **Oxford Nanopore** and **PacBio**. It supports both canonical base DNA and modified base calling, including specialized applications such as **Fiber-seq**.\n\nThis **end-to-end pipeline** handles the entire workflow β€” **from raw read processing and alignment, to comprehensive somatic variant calling**, including single nucleotide variants, indels, structural variants, copy number alterations, and modified bases.\n\nIt can be run in both **matched tumour-normal** and **tumour-only mode**, offering flexibility depending on the users study design.\n\nDeveloped using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.\n\nFor more information on how to run the pipeline, you can also go [here](https://intgenomicslab.github.io/lrsomatic).\n\n## Pipeline summary\n\n![image](./assets/lrsomatic_1.0.png)\n\n**1) Pre-processing:**\n\na. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))\n\nb. Alignment to the reference genome ([`minimap2`](https://github.com/lh3/minimap2))\n\nc. Post alignment QC ([`cramino`](https://github.com/wdecoster/cramino), [`samtools idxstats`](https://github.com/samtools/samtools), [`samtools flagstats`](https://github.com/samtools/samtools), [`samtools stats`](https://github.com/samtools/samtools))\n\nd. Specific for calling modified base calling ([`Modkit`](https://github.com/nanoporetech/modkit), [`Fibertools`](https://github.com/fiberseq/fibertools-rs))\n\n**2i) Matched mode: small variant calling:**\n\na. Calling Germline SNPs ([`Clair3`](https://github.com/HKU-BAL/Clair3))\n\nb. Phasing and Haplotagging the SNPs in the normal and tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\nc. Calling somatic SNVs ([`ClairS`](https://github.com/HKU-BAL/ClairS))\n\n**2ii) Tumour only mode: small variant calling:**\n\na. Calling Germline SNPs and somatic SNVs ([`ClairS-TO`](https://github.com/HKU-BAL/ClairS-TO))\n\nb. Phasing and Haplotagging germline SNPs in tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\n**3) Large variant calling:**\n\na. Somatic structural variant calling ([`Severus`](https://github.com/KolmogorovLab/Severus))\n\nb. Somatic structural variant and copy-number calling ([`SAVANA`](https://github.com/cortes-ciriano-lab/savana))\n\nc. Copy number alterion calling; long read version of ([`ASCAT`](https://github.com/VanLoo-lab/ascat))\n\n**4) Annotation:**\n\na. Small variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep)), with pathogenicity and clinical-significance plugins: [`AlphaMissense`](https://github.com/google-deepmind/alphamissense), [`ClinVar`](https://www.ncbi.nlm.nih.gov/clinvar/), [`REVEL`](https://sites.google.com/site/revelgenomics/), [`SIFT`/`PolyPhen`](https://github.com/Ensembl/VEP_plugins), and optionally [`CADD`](https://cadd.gs.washington.edu/) and [`EVE`](https://evemodel.org/)\n\nb. Structural variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\nc. Somatic SV and CNA functional annotation ([`Padfoot`](https://github.com/KolmogorovLab/Padfoot))\n\n**5) Visualisation:**\n\na. Rearrangement and copy-number figures per CN/SV caller pair ([`ReConPlot`](https://github.com/cortes-ciriano-lab/ReConPlot))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst prepare a samplesheet with your input data that looks as follows:\n\n```csv\nsample,bam_tumor,bam_normal,platform,sex,fiber\nsample1,tumour.bam,normal.bam,ont,female,n\nsample2,tumour.bam,,ont,female,y\nsample3,tumour.bam,,pb,male,n\nsample4,tumour.bam,normal.bam,pb,male,y\n```\n\nEach row is a sample. BAMs must be unaligned, all fields except `bam_normal` are required, and an empty `bam_normal` runs the sample in tumour-only mode. `platform` is `ont` or `pb`, `sex` is `female` or `male`, and `fiber` is `y` or `n` for Fiber-seq; see the [usage documentation](/docs/usage.md#full-description-of-samplesheet-columns).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\nMore detail is given in our [usage documentation](/docs/usage.md)\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Amber Verhasselt, Alexandra PančíkovΓ‘, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester.\n\n## Pipeline output\n\nThe main output is an aligned and phased tumour BAM, per-sample QC from `cramino`, `mosdepth`, `samtools` and optionally `fibertools`, a MultiQC report, and a self-contained per-sample HTML report (`/report/_report.html`; disable it with `--skip_report`).\n\nVariant and copy number callers (`clairS`, `clairS-TO`, `severus`, `savana`, `ascat`) write to their own folders; Padfoot annotations and ReConPlot figures go to `padfoot/` and `reconplot/`, one subfolder per caller pair. See the [output documentation](/docs/output.md).\n\nExample output directory structure:\n\n```\nβ”œβ”€β”€ Sample 1\nβ”‚ β”œβ”€β”€ ascat\nβ”‚ β”œβ”€β”€ bamfiles\nβ”‚ β”œβ”€β”€ padfoot\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”‚ └── severus_wakhan\nβ”‚ β”œβ”€β”€ qc\nβ”‚ β”‚ β”œβ”€β”€ tumor\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_aln\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_ubam\nβ”‚ β”‚ β”‚ β”œβ”€β”€ fibertoolsrs\nβ”‚ β”‚ β”‚ β”œβ”€β”€ mosdepth\nβ”‚ β”‚ β”‚ β”œβ”€β”€ samtools\nβ”‚ β”œβ”€β”€ reconplot\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”‚ β”œβ”€β”€ severus_ascat\nβ”‚ β”‚ └── severus_wakhan\nβ”‚ β”œβ”€β”€ variants\nβ”‚ β”‚ β”œβ”€β”€clairS-TO\nβ”‚ β”‚ β”œβ”€β”€severus\nβ”‚ β”‚ β”œβ”€β”€savana\nβ”‚ β”œβ”€β”€ vep\nβ”‚ β”‚ β”œβ”€β”€ germline\nβ”‚ β”‚ β”œβ”€β”€ somatic\nβ”‚ β”‚ β”œβ”€β”€ SVs\nβ”‚ β”œβ”€β”€ report\nβ”‚\nβ”œβ”€β”€ Sample 2\nβ”‚ β”œβ”€β”€ ascat\nβ”‚ β”œβ”€β”€ bamfiles\nβ”‚ β”œβ”€β”€ padfoot\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”‚ └── severus_wakhan\nβ”‚ β”œβ”€β”€ qc\nβ”‚ β”‚ β”œβ”€β”€ tumor\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_aln\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_ubam\nβ”‚ β”‚ β”‚ β”œβ”€β”€ fibertoolsrs\nβ”‚ β”‚ β”‚ β”œβ”€β”€ mosdepth\nβ”‚ β”‚ β”‚ β”œβ”€β”€ samtools\nβ”‚ β”‚ β”œβ”€β”€ normal\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_aln\nβ”‚ β”‚ β”‚ β”œβ”€β”€ cramino_ubam\nβ”‚ β”‚ β”‚ β”œβ”€β”€ fibertoolsrs\nβ”‚ β”‚ β”‚ β”œβ”€β”€ mosdepth\nβ”‚ β”‚ β”‚ β”œβ”€β”€ samtools\nβ”‚ β”œβ”€β”€ reconplot\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”‚ β”œβ”€β”€ severus_ascat\nβ”‚ β”‚ └── severus_wakhan\nβ”‚ β”œβ”€β”€ variants\nβ”‚ β”‚ β”œβ”€β”€ clair3\nβ”‚ β”‚ β”œβ”€β”€ clairS\nβ”‚ β”‚ β”œβ”€β”€ severus\nβ”‚ β”‚ β”œβ”€β”€ savana\nβ”‚ β”œβ”€β”€ vep\nβ”‚ β”‚ β”œβ”€β”€ germline\nβ”‚ β”‚ β”œβ”€β”€ somatic\nβ”‚ β”‚ β”œβ”€β”€ SVs\nβ”œβ”€β”€ pipeline_info\n```\n\nmore detail is given in our [output documentation](/docs/output.md)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\nIf you use `IntGenomicsLab/lrsomatic` for your analysis, please cite it using the following:\n\n> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data\n>\n> Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-LucΓ­a Rocha IraizΓ³s, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester\n>\n> bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -93,7 +93,7 @@ }, "mentions": [ { - "@id": "#97291dab-36c6-4b95-b3ba-9d715c953af5" + "@id": "#a31a4ee9-5087-4832-8fbd-821dbf0fc102" } ], "name": "IntGenomicsLab/lrsomatic" @@ -144,7 +144,7 @@ } ], "dateCreated": "", - "dateModified": "2026-10-28T10:47:28Z", + "dateModified": "2026-10-29T13:23:13Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -172,10 +172,10 @@ }, "url": [ "https://github.com/IntGenomicsLab/lrsomatic", - "https://nf-co.re/IntGenomicsLab/lrsomatic/1.1.0/" + "https://nf-co.re/IntGenomicsLab/lrsomatic/dev/" ], "version": [ - "1.1.0" + "1.2.0dev" ] }, { @@ -200,11 +200,11 @@ "version": "1.1" }, { - "@id": "#97291dab-36c6-4b95-b3ba-9d715c953af5", + "@id": "#a31a4ee9-5087-4832-8fbd-821dbf0fc102", "@type": "TestSuite", "instance": [ { - "@id": "#65d87ca4-0d27-4af3-8b1a-875becab8174" + "@id": "#1e5ff16e-ac97-4932-ac17-6abc6d495529" } ], "mainEntity": { @@ -222,7 +222,7 @@ "version": "0.2" }, { - "@id": "#65d87ca4-0d27-4af3-8b1a-875becab8174", + "@id": "#1e5ff16e-ac97-4932-ac17-6abc6d495529", "@type": "TestInstance", "name": "GitHub Actions workflow for testing IntGenomicsLab/lrsomatic", "resource": "repos/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml", diff --git a/subworkflows/local/deepsomatic.nf b/subworkflows/local/deepsomatic/main.nf similarity index 90% rename from subworkflows/local/deepsomatic.nf rename to subworkflows/local/deepsomatic/main.nf index 1bb5d86c..58acf3d4 100644 --- a/subworkflows/local/deepsomatic.nf +++ b/subworkflows/local/deepsomatic/main.nf @@ -1,6 +1,6 @@ -include { DEEPSOMATIC_MAKEEXAMPLES } from '../../modules/local/deepsomatic/makeexamples/main' -include { DEEPSOMATIC_CALLVARIANTS } from '../../modules/local/deepsomatic/callvariants/main' -include { DEEPSOMATIC_POSTPROCESSVARIANTS } from '../../modules/local/deepsomatic/postprocessvariants/main' +include { DEEPSOMATIC_MAKEEXAMPLES } from '../../../modules/local/deepsomatic/makeexamples/main' +include { DEEPSOMATIC_CALLVARIANTS } from '../../../modules/local/deepsomatic/callvariants/main' +include { DEEPSOMATIC_POSTPROCESSVARIANTS } from '../../../modules/local/deepsomatic/postprocessvariants/main' workflow DEEPSOMATIC { take: diff --git a/subworkflows/local/dmr.nf b/subworkflows/local/dmr/main.nf similarity index 92% rename from subworkflows/local/dmr.nf rename to subworkflows/local/dmr/main.nf index 5d869c26..e7bea406 100644 --- a/subworkflows/local/dmr.nf +++ b/subworkflows/local/dmr/main.nf @@ -1,8 +1,8 @@ // IMPORT MODULES -include { HTSLIB_BGZIPTABIX } from '../../modules/nf-core/htslib/bgziptabix/main' -include { MODKIT_DMR } from '../../modules/nf-core/modkit/dmr/main' -include { DMR_HAPLOTYPE_REGIONS } from '../../modules/local/dmr/haplotype_regions/main' -include { DMR_NEAREST_GENE } from '../../modules/local/dmr/nearest_gene/main' +include { HTSLIB_BGZIPTABIX } from '../../../modules/nf-core/htslib/bgziptabix/main' +include { MODKIT_DMR } from '../../../modules/nf-core/modkit/dmr/main' +include { DMR_HAPLOTYPE_REGIONS } from '../../../modules/local/dmr/haplotype_regions/main' +include { DMR_NEAREST_GENE } from '../../../modules/local/dmr/nearest_gene/main' workflow DMR { diff --git a/subworkflows/local/ecdna.nf b/subworkflows/local/ecdna/main.nf similarity index 91% rename from subworkflows/local/ecdna.nf rename to subworkflows/local/ecdna/main.nf index 2c39d5af..02dcfbd2 100644 --- a/subworkflows/local/ecdna.nf +++ b/subworkflows/local/ecdna/main.nf @@ -3,12 +3,12 @@ // // IMPORT MODULES -include { ASCAT_TO_CORAL_BED } from '../../modules/local/ascattocoralbed/main' -include { CORAL_SEED } from '../../modules/local/coral/seed/main' -include { CORAL_RECONSTRUCT } from '../../modules/local/coral/reconstruct/main' -include { CORAL_CYCLE } from '../../modules/local/coral/cycle/main' -include { CORAL_PLOT } from '../../modules/local/coral/plot/main' -include { AMPLICONCLASSIFIER } from '../../modules/local/ampliconclassifier/main' +include { ASCAT_TO_CORAL_BED } from '../../../modules/local/ascattocoralbed/main' +include { CORAL_SEED } from '../../../modules/local/coral/seed/main' +include { CORAL_RECONSTRUCT } from '../../../modules/local/coral/reconstruct/main' +include { CORAL_CYCLE } from '../../../modules/local/coral/cycle/main' +include { CORAL_PLOT } from '../../../modules/local/coral/plot/main' +include { AMPLICONCLASSIFIER } from '../../../modules/local/ampliconclassifier/main' workflow ECDNA { diff --git a/subworkflows/local/fiberseq.nf b/subworkflows/local/fiberseq/main.nf similarity index 93% rename from subworkflows/local/fiberseq.nf rename to subworkflows/local/fiberseq/main.nf index abe94da8..0e5a8501 100644 --- a/subworkflows/local/fiberseq.nf +++ b/subworkflows/local/fiberseq/main.nf @@ -2,10 +2,10 @@ // Fiber-seq: m6A prediction (PacBio with kinetics), nucleosome and FIRE calling on the unaligned BAMs // -include { FIBERTOOLSRS_PREDICTM6A } from '../../modules/local/fibertoolsrs/predictm6a' -include { FIBERTOOLSRS_FIRE } from '../../modules/local/fibertoolsrs/fire' -include { FIBERTOOLSRS_NUCLEOSOMES } from '../../modules/local/fibertoolsrs/nucleosomes' -include { FIBERTOOLSRS_QC } from '../../modules/local/fibertoolsrs/qc' +include { FIBERTOOLSRS_PREDICTM6A } from '../../../modules/local/fibertoolsrs/predictm6a' +include { FIBERTOOLSRS_FIRE } from '../../../modules/local/fibertoolsrs/fire' +include { FIBERTOOLSRS_NUCLEOSOMES } from '../../../modules/local/fibertoolsrs/nucleosomes' +include { FIBERTOOLSRS_QC } from '../../../modules/local/fibertoolsrs/qc' workflow FIBERSEQ { diff --git a/subworkflows/local/padfoot_annotation.nf b/subworkflows/local/padfoot_annotation/main.nf similarity index 94% rename from subworkflows/local/padfoot_annotation.nf rename to subworkflows/local/padfoot_annotation/main.nf index 852d0a87..3cf487dc 100644 --- a/subworkflows/local/padfoot_annotation.nf +++ b/subworkflows/local/padfoot_annotation/main.nf @@ -1,6 +1,6 @@ // IMPORT MODULES -include { PADFOOT as PADFOOT_SEVERUS_WAKHAN } from '../../modules/local/padfoot/main' -include { PADFOOT as PADFOOT_SAVANA } from '../../modules/local/padfoot/main' +include { PADFOOT as PADFOOT_SEVERUS_WAKHAN } from '../../../modules/local/padfoot/main' +include { PADFOOT as PADFOOT_SAVANA } from '../../../modules/local/padfoot/main' // // Padfoot annotation of somatic SVs + CNAs, once per caller pair that produced output for a sample: diff --git a/subworkflows/local/paired/paired_smallvar_germline.nf b/subworkflows/local/paired/paired_smallvar_germline.nf index f1ba424d..f1dc9cb7 100644 --- a/subworkflows/local/paired/paired_smallvar_germline.nf +++ b/subworkflows/local/paired/paired_smallvar_germline.nf @@ -5,7 +5,7 @@ include { CLAIR3 } from '../../../modules/local/clair3/main.n // IMPORT SUBWORKFLOWS include { DEEPVARIANT } from '../../../subworkflows/nf-core/deepvariant/main.nf' -include { SMALL_VARIANT_CONSENSUS as GERMLINE_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus.nf' +include { SMALL_VARIANT_CONSENSUS as GERMLINE_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus/main.nf' workflow PAIRED_SMALLVAR_GERMLINE { diff --git a/subworkflows/local/paired/paired_smallvar_somatic.nf b/subworkflows/local/paired/paired_smallvar_somatic.nf index 5a499ec0..7bcf5258 100644 --- a/subworkflows/local/paired/paired_smallvar_somatic.nf +++ b/subworkflows/local/paired/paired_smallvar_somatic.nf @@ -6,8 +6,8 @@ include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/co include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort' // IMPORT SUBWORKFLOWS -include { DEEPSOMATIC } from '../../../subworkflows/local/deepsomatic.nf' -include { SMALL_VARIANT_CONSENSUS as SOMATIC_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus.nf' +include { DEEPSOMATIC } from '../../../subworkflows/local/deepsomatic/main.nf' +include { SMALL_VARIANT_CONSENSUS as SOMATIC_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus/main.nf' workflow PAIRED_SMALLVAR_SOMATIC { diff --git a/subworkflows/local/phasing_haplotyping.nf b/subworkflows/local/phasing_haplotyping/main.nf similarity index 95% rename from subworkflows/local/phasing_haplotyping.nf rename to subworkflows/local/phasing_haplotyping/main.nf index 9324a986..f974e510 100644 --- a/subworkflows/local/phasing_haplotyping.nf +++ b/subworkflows/local/phasing_haplotyping/main.nf @@ -1,22 +1,22 @@ // Import modules -include { LONGPHASE_PHASE as LONGPHASE_PHASE_GERMLINE } from '../../modules/nf-core/longphase/phase/main.nf' -include { LONGPHASE_PHASE as LONGPHASE_PHASE_SOMATIC } from '../../modules/nf-core/longphase/phase/main.nf' -include { LONGPHASE_HAPLOTAG } from '../../modules/nf-core/longphase/haplotag/main.nf' -include { LONGPHASE_MODCALL as LONGPHASE_MODCALL_GERMLINE } from '../../modules/local/longphase/modcall/main.nf' -include { LONGPHASE_MODCALL as LONGPHASE_MODCALL_SOMATIC } from '../../modules/local/longphase/modcall/main.nf' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main.nf' -include { BCFTOOLS_CONCAT } from '../../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_CONCAT as CONCAT_SOMATIC_UNPHASED } from '../../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_SORT } from '../../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_SORT as SORT_SOMATIC_PHASED } from '../../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_VIEW } from '../../modules/local/bcftools/view/main.nf' -include { BCFTOOLS_VIEW as SOMATIC_ALT } from '../../modules/local/bcftools/view/main.nf' -include { BCFTOOLS_VIEW as SOMATIC_NONALT } from '../../modules/local/bcftools/view/main.nf' -include { BCFTOOLS_EXCLUDE_SITES as GERMLINE_ANCHORS } from '../../modules/local/bcftools/excludesites/main.nf' -include { BCFTOOLS_NORM as REJOIN_SOMATIC } from '../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_NORM as REJOIN_GERMLINE } from '../../modules/nf-core/bcftools/norm/main' -include { VCFTAG as TAG_SOMATIC } from '../../modules/local/vcftag/main.nf' -include { VCFTAG as TAG_GERMLINE } from '../../modules/local/vcftag/main.nf' +include { LONGPHASE_PHASE as LONGPHASE_PHASE_GERMLINE } from '../../../modules/nf-core/longphase/phase/main.nf' +include { LONGPHASE_PHASE as LONGPHASE_PHASE_SOMATIC } from '../../../modules/nf-core/longphase/phase/main.nf' +include { LONGPHASE_HAPLOTAG } from '../../../modules/nf-core/longphase/haplotag/main.nf' +include { LONGPHASE_MODCALL as LONGPHASE_MODCALL_GERMLINE } from '../../../modules/local/longphase/modcall/main.nf' +include { LONGPHASE_MODCALL as LONGPHASE_MODCALL_SOMATIC } from '../../../modules/local/longphase/modcall/main.nf' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main.nf' +include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat/main' +include { BCFTOOLS_CONCAT as CONCAT_SOMATIC_UNPHASED } from '../../../modules/nf-core/bcftools/concat/main' +include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main' +include { BCFTOOLS_SORT as SORT_SOMATIC_PHASED } from '../../../modules/nf-core/bcftools/sort/main' +include { BCFTOOLS_VIEW } from '../../../modules/local/bcftools/view/main.nf' +include { BCFTOOLS_VIEW as SOMATIC_ALT } from '../../../modules/local/bcftools/view/main.nf' +include { BCFTOOLS_VIEW as SOMATIC_NONALT } from '../../../modules/local/bcftools/view/main.nf' +include { BCFTOOLS_EXCLUDE_SITES as GERMLINE_ANCHORS } from '../../../modules/local/bcftools/excludesites/main.nf' +include { BCFTOOLS_NORM as REJOIN_SOMATIC } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_NORM as REJOIN_GERMLINE } from '../../../modules/nf-core/bcftools/norm/main' +include { VCFTAG as TAG_SOMATIC } from '../../../modules/local/vcftag/main.nf' +include { VCFTAG as TAG_GERMLINE } from '../../../modules/local/vcftag/main.nf' workflow PHASING_HAPLOTYPING { diff --git a/subworkflows/local/prepare_aa_data_repo.nf b/subworkflows/local/prepare_aa_data_repo/main.nf similarity index 92% rename from subworkflows/local/prepare_aa_data_repo.nf rename to subworkflows/local/prepare_aa_data_repo/main.nf index 8d3cf924..84785063 100644 --- a/subworkflows/local/prepare_aa_data_repo.nf +++ b/subworkflows/local/prepare_aa_data_repo/main.nf @@ -2,8 +2,8 @@ // Stage the AmpliconArchitect data repository AmpliconClassifier reads at runtime // -include { AADATAREPO_DOWNLOAD } from '../../modules/local/aadatarepo/download/main' -include { UNTAR as UNTAR_AA_DATA_REPO } from '../../modules/nf-core/untar/main' +include { AADATAREPO_DOWNLOAD } from '../../../modules/local/aadatarepo/download/main' +include { UNTAR as UNTAR_AA_DATA_REPO } from '../../../modules/nf-core/untar/main' workflow PREPARE_AA_DATA_REPO { diff --git a/subworkflows/local/prepare_annotation.nf b/subworkflows/local/prepare_annotation/main.nf similarity index 96% rename from subworkflows/local/prepare_annotation.nf rename to subworkflows/local/prepare_annotation/main.nf index 114199a3..e5fe96a7 100644 --- a/subworkflows/local/prepare_annotation.nf +++ b/subworkflows/local/prepare_annotation/main.nf @@ -1,4 +1,4 @@ -include {ENSEMBLVEP_DOWNLOAD } from '../../modules/nf-core/ensemblvep/download/main.nf' +include {ENSEMBLVEP_DOWNLOAD } from '../../../modules/nf-core/ensemblvep/download/main.nf' workflow PREPARE_ANNOTATION { diff --git a/subworkflows/local/prepare_reference_files.nf b/subworkflows/local/prepare_reference_files/main.nf similarity index 93% rename from subworkflows/local/prepare_reference_files.nf rename to subworkflows/local/prepare_reference_files/main.nf index 3a105744..b5ef904e 100644 --- a/subworkflows/local/prepare_reference_files.nf +++ b/subworkflows/local/prepare_reference_files/main.nf @@ -2,13 +2,13 @@ // Prepare reference files (unzipping and adding index) // -include { PIGZ_UNCOMPRESS as UNZIP_FASTA } from '../../modules/nf-core/pigz/uncompress/main' -include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' -include { UNZIP as UNZIP_ALLELES } from '../../modules/nf-core/unzip/main' -include { UNZIP as UNZIP_GC } from '../../modules/nf-core/unzip/main' -include { UNZIP as UNZIP_LOCI } from '../../modules/nf-core/unzip/main' -include { UNZIP as UNZIP_RT } from '../../modules/nf-core/unzip/main' -include { CLAIR3_MODEL } from '../../modules/local/clair3_model/main' +include { PIGZ_UNCOMPRESS as UNZIP_FASTA } from '../../../modules/nf-core/pigz/uncompress/main' +include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' +include { UNZIP as UNZIP_ALLELES } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_GC } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_LOCI } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_RT } from '../../../modules/nf-core/unzip/main' +include { CLAIR3_MODEL } from '../../../modules/local/clair3_model/main' workflow PREPARE_REFERENCE_FILES { take: diff --git a/subworkflows/local/prepare_signatures.nf b/subworkflows/local/prepare_signatures/main.nf similarity index 94% rename from subworkflows/local/prepare_signatures.nf rename to subworkflows/local/prepare_signatures/main.nf index 11cfc3d4..6209b6e1 100644 --- a/subworkflows/local/prepare_signatures.nf +++ b/subworkflows/local/prepare_signatures/main.nf @@ -1,5 +1,5 @@ -include { SIGPROFILER_INSTALL } from '../../modules/local/sigprofiler/install/main' -include { SIGPROFILER_VERIFY } from '../../modules/local/sigprofiler/verify/main' +include { SIGPROFILER_INSTALL } from '../../../modules/local/sigprofiler/install/main' +include { SIGPROFILER_VERIFY } from '../../../modules/local/sigprofiler/verify/main' workflow PREPARE_SIGNATURES { diff --git a/subworkflows/local/prepare_vep_plugins.nf b/subworkflows/local/prepare_vep_plugins/main.nf similarity index 86% rename from subworkflows/local/prepare_vep_plugins.nf rename to subworkflows/local/prepare_vep_plugins/main.nf index 0b8245d7..9dcfe6cd 100644 --- a/subworkflows/local/prepare_vep_plugins.nf +++ b/subworkflows/local/prepare_vep_plugins/main.nf @@ -3,13 +3,13 @@ // ClinVar once so the VEP tasks never stage it from its host themselves // -include { UNZIP as UNZIP_REVEL } from '../../modules/nf-core/unzip/main.nf' -include { UNZIP as UNZIP_EVE } from '../../modules/nf-core/unzip/main.nf' -include { WGET as WGET_REVEL } from '../../modules/nf-core/wget/main' -include { WGET as WGET_EVE } from '../../modules/nf-core/wget/main' -include { VEPPLUGIN_REVEL } from '../../modules/local/vepplugin/revel/main.nf' -include { VEPPLUGIN_EVE } from '../../modules/local/vepplugin/eve/main.nf' -include { VEPPLUGIN_CLINVAR } from '../../modules/local/vepplugin/clinvar/main.nf' +include { UNZIP as UNZIP_REVEL } from '../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_EVE } from '../../../modules/nf-core/unzip/main.nf' +include { WGET as WGET_REVEL } from '../../../modules/nf-core/wget/main' +include { WGET as WGET_EVE } from '../../../modules/nf-core/wget/main' +include { VEPPLUGIN_REVEL } from '../../../modules/local/vepplugin/revel/main.nf' +include { VEPPLUGIN_EVE } from '../../../modules/local/vepplugin/eve/main.nf' +include { VEPPLUGIN_CLINVAR } from '../../../modules/local/vepplugin/clinvar/main.nf' workflow PREPARE_VEP_PLUGINS { diff --git a/subworkflows/local/reconplot_figures.nf b/subworkflows/local/reconplot_figures/main.nf similarity index 94% rename from subworkflows/local/reconplot_figures.nf rename to subworkflows/local/reconplot_figures/main.nf index 0057a07d..cdb1575c 100644 --- a/subworkflows/local/reconplot_figures.nf +++ b/subworkflows/local/reconplot_figures/main.nf @@ -1,7 +1,7 @@ // IMPORT MODULES -include { RECONPLOT as RECONPLOT_SEVERUS_ASCAT } from '../../modules/local/reconplot/main' -include { RECONPLOT as RECONPLOT_SEVERUS_WAKHAN } from '../../modules/local/reconplot/main' -include { RECONPLOT as RECONPLOT_SAVANA } from '../../modules/local/reconplot/main' +include { RECONPLOT as RECONPLOT_SEVERUS_ASCAT } from '../../../modules/local/reconplot/main' +include { RECONPLOT as RECONPLOT_SEVERUS_WAKHAN } from '../../../modules/local/reconplot/main' +include { RECONPLOT as RECONPLOT_SAVANA } from '../../../modules/local/reconplot/main' // // ReConPlot rearrangement + copy-number figures for every CN/SV caller pair that produced output for diff --git a/subworkflows/local/small_variant_consensus.nf b/subworkflows/local/small_variant_consensus/main.nf similarity index 96% rename from subworkflows/local/small_variant_consensus.nf rename to subworkflows/local/small_variant_consensus/main.nf index 773609fd..83b7a712 100644 --- a/subworkflows/local/small_variant_consensus.nf +++ b/subworkflows/local/small_variant_consensus/main.nf @@ -1,11 +1,11 @@ -include { BCFTOOLS_NORM } from '../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_NORM as BCFTOOLS_NORM_REJOIN } from '../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_ISEC } from '../../modules/nf-core/bcftools/isec/main' -include { BCFTOOLS_QUERY } from '../../modules/nf-core/bcftools/query/main' -include { BCFTOOLS_ANNOTATE } from '../../modules/nf-core/bcftools/annotate/main' -include { BCFTOOLS_SORT as SORT_POST_NORM } from '../../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_SORT as BCFTOOLS_SORT_CONSENSUS } from '../../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_CALLER_UNION } from '../../modules/local/bcftools/callerunion/main' +include { BCFTOOLS_NORM } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_NORM as BCFTOOLS_NORM_REJOIN } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_ISEC } from '../../../modules/nf-core/bcftools/isec/main' +include { BCFTOOLS_QUERY } from '../../../modules/nf-core/bcftools/query/main' +include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' +include { BCFTOOLS_SORT as SORT_POST_NORM } from '../../../modules/nf-core/bcftools/sort/main' +include { BCFTOOLS_SORT as BCFTOOLS_SORT_CONSENSUS } from '../../../modules/nf-core/bcftools/sort/main' +include { BCFTOOLS_CALLER_UNION } from '../../../modules/local/bcftools/callerunion/main' diff --git a/subworkflows/local/tests/dmr.nf.test b/subworkflows/local/tests/dmr.nf.test index d8a88a05..a7c79909 100644 --- a/subworkflows/local/tests/dmr.nf.test +++ b/subworkflows/local/tests/dmr.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Workflow DMR" - script "../dmr.nf" + script "../dmr/main.nf" workflow "DMR" config "./nextflow.config" diff --git a/subworkflows/local/tests/ecdna.nf.test b/subworkflows/local/tests/ecdna.nf.test index 0e7f8539..19bda0a6 100644 --- a/subworkflows/local/tests/ecdna.nf.test +++ b/subworkflows/local/tests/ecdna.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Subworkflow ECDNA" - script "../ecdna.nf" + script "../ecdna/main.nf" workflow "ECDNA" tag "subworkflows" diff --git a/subworkflows/local/tests/padfoot_annotation.nf.test b/subworkflows/local/tests/padfoot_annotation.nf.test index 5d53a0ca..f6008088 100644 --- a/subworkflows/local/tests/padfoot_annotation.nf.test +++ b/subworkflows/local/tests/padfoot_annotation.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Workflow PADFOOT_ANNOTATION" - script "../padfoot_annotation.nf" + script "../padfoot_annotation/main.nf" workflow "PADFOOT_ANNOTATION" tag "subworkflows" diff --git a/subworkflows/local/tests/prepare_aa_data_repo.nf.test b/subworkflows/local/tests/prepare_aa_data_repo.nf.test index c2910f67..5c45f98d 100644 --- a/subworkflows/local/tests/prepare_aa_data_repo.nf.test +++ b/subworkflows/local/tests/prepare_aa_data_repo.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Subworkflow PREPARE_AA_DATA_REPO" - script "../prepare_aa_data_repo.nf" + script "../prepare_aa_data_repo/main.nf" workflow "PREPARE_AA_DATA_REPO" tag "subworkflows" diff --git a/subworkflows/local/tests/prepare_signatures.nf.test b/subworkflows/local/tests/prepare_signatures.nf.test index 3ea7f829..4e53a1b8 100644 --- a/subworkflows/local/tests/prepare_signatures.nf.test +++ b/subworkflows/local/tests/prepare_signatures.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Workflow PREPARE_SIGNATURES" - script "../prepare_signatures.nf" + script "../prepare_signatures/main.nf" workflow "PREPARE_SIGNATURES" tag "subworkflows" diff --git a/subworkflows/local/tests/reconplot_figures.nf.test b/subworkflows/local/tests/reconplot_figures.nf.test index 2c9fbd3b..2217b559 100644 --- a/subworkflows/local/tests/reconplot_figures.nf.test +++ b/subworkflows/local/tests/reconplot_figures.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Workflow RECONPLOT_FIGURES" - script "../reconplot_figures.nf" + script "../reconplot_figures/main.nf" workflow "RECONPLOT_FIGURES" tag "subworkflows" diff --git a/subworkflows/local/tumor_only/tumoronly_smallvar.nf b/subworkflows/local/tumor_only/tumoronly_smallvar.nf index 24c67719..b69d5a40 100644 --- a/subworkflows/local/tumor_only/tumoronly_smallvar.nf +++ b/subworkflows/local/tumor_only/tumoronly_smallvar.nf @@ -7,9 +7,9 @@ include { VCFSPLIT } from '../../../modules/local/vcfsplit/main // IMPORT SUBWORKFLOWS include { DEEPVARIANT } from '../../../subworkflows/nf-core/deepvariant/main.nf' -include { DEEPSOMATIC } from '../../../subworkflows/local/deepsomatic.nf' -include { SMALL_VARIANT_CONSENSUS as GERMLINE_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus.nf' -include { SMALL_VARIANT_CONSENSUS as SOMATIC_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus.nf' +include { DEEPSOMATIC } from '../../../subworkflows/local/deepsomatic/main.nf' +include { SMALL_VARIANT_CONSENSUS as GERMLINE_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus/main.nf' +include { SMALL_VARIANT_CONSENSUS as SOMATIC_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus/main.nf' // Germline verdict transfer: DeepSomatic adjudicates DeepVariant's tumor-derived germline calls. include { BCFTOOLS_NORM as DS_VERDICT_SPLIT_DS } from '../../../modules/nf-core/bcftools/norm/main' diff --git a/tests/chm13.nf.test.snap b/tests/chm13.nf.test.snap index 1e1877ae..fd474c86 100644 --- a/tests/chm13.nf.test.snap +++ b/tests/chm13.nf.test.snap @@ -159,7 +159,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } } ], diff --git a/tests/clair_only.nf.test.snap b/tests/clair_only.nf.test.snap index 9bff949b..a7762429 100644 --- a/tests/clair_only.nf.test.snap +++ b/tests/clair_only.nf.test.snap @@ -166,7 +166,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ diff --git a/tests/consensus.nf.test.snap b/tests/consensus.nf.test.snap index d641c78e..748289dd 100644 --- a/tests/consensus.nf.test.snap +++ b/tests/consensus.nf.test.snap @@ -210,7 +210,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ diff --git a/tests/deep_only.nf.test.snap b/tests/deep_only.nf.test.snap index 4a9f4862..235e658b 100644 --- a/tests/deep_only.nf.test.snap +++ b/tests/deep_only.nf.test.snap @@ -171,7 +171,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 810824dd..72ffa7e8 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -147,7 +147,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ diff --git a/tests/nextflow.config b/tests/nextflow.config index 0ad47f65..fc33809d 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,8 +4,6 @@ ======================================================================================== */ -// TODO nf-core: Specify any additional parameters here -// Or any resources requirements params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/lrsomatic' diff --git a/tests/union.nf.test.snap b/tests/union.nf.test.snap index 274fbb7b..0602876a 100644 --- a/tests/union.nf.test.snap +++ b/tests/union.nf.test.snap @@ -204,7 +204,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ From d038cf94d18a138e1022e0a293cc0d4d17373250 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 29 Oct 2026 14:22:40 +0100 Subject: [PATCH 06/10] Fill in PR number in CHANGELOG entry Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6cf736d6..cdaf8702 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- [#PR](https://github.com/IntGenomicsLab/lrsomatic/pull/PR) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` is now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). +- [#227](https://github.com/IntGenomicsLab/lrsomatic/pull/227) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` is now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, sets `manifest.diagram` to the existing metro map (`assets/lrsomatic_1.0.png`), replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). - [#204](https://github.com/IntGenomicsLab/lrsomatic/pull/204) - With `--modkit_phased` set and haplotype DMR running, `5hmC` is appended to `--modified-bases` whenever `--modkit_args` names `5mC` without it, so the published `modkit_pileup/*_{hp1,hp2,combined}.bed.gz` now carry a 5hmC row next to each 5mC row. `modkit dmr pair` rejects bedMethyl rows whose valid coverage includes uncounted (`N_other`) calls, which ONT SUP data calling both 5mC and 5hmC produces under the `--cpg --modified-bases 5mC` default. Runs with `--skip_dmr`, without `--modkit_phased`, or without DMR references keep `--modkit_args` exactly as given (@YannVRB). From 8f0714a4a3335271011335a578ec6106a2ff6e03 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Mon, 2 Nov 2026 14:31:08 +0100 Subject: [PATCH 07/10] Address #227 review: boolean autocorrelation, version sync, extended list - autocorrelation is now a boolean defaulting to false (schema and nextflow.config), matching docs/usage.md. A bare --autocorrelation flag now validates, and --autocorrelation false no longer contradicts the description. - .nf-core.yml template.version 1.1.0 -> 1.2.0dev, matching manifest.version (version_consistency: "Version tags are consistent"). - CONTRIBUTING: refer to all tests tagged `extended` and list chm13. Co-Authored-By: Claude Opus 5.5 --- .nf-core.yml | 2 +- CHANGELOG.md | 2 +- docs/CONTRIBUTING.md | 2 +- nextflow.config | 2 +- nextflow_schema.json | 5 +++-- 5 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 80c387b7..f1bc5f3e 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -44,4 +44,4 @@ template: outdir: . skip_features: - fastqc - version: 1.1.0 + version: 1.2.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index cdaf8702..576c1250 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- [#227](https://github.com/IntGenomicsLab/lrsomatic/pull/227) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` is now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). +- [#227](https://github.com/IntGenomicsLab/lrsomatic/pull/227) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` and the `.nf-core.yml` template version are now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; `--autocorrelation` is now a boolean (default `false`), as `docs/usage.md` already described it, so a bare `--autocorrelation` flag passes validation; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, sets `manifest.diagram` to the existing metro map (`assets/lrsomatic_1.0.png`), replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). - [#204](https://github.com/IntGenomicsLab/lrsomatic/pull/204) - With `--modkit_phased` set and haplotype DMR running, `5hmC` is appended to `--modified-bases` whenever `--modkit_args` names `5mC` without it, so the published `modkit_pileup/*_{hp1,hp2,combined}.bed.gz` now carry a 5hmC row next to each 5mC row. `modkit dmr pair` rejects bedMethyl rows whose valid coverage includes uncounted (`N_other`) calls, which ONT SUP data calling both 5mC and 5hmC produces under the `--cpg --modified-bases 5mC` default. Runs with `--skip_dmr`, without `--modkit_phased`, or without DMR references keep `--modkit_args` exactly as given (@YannVRB). diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 97a76586..cd5eb2f8 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -166,4 +166,4 @@ If you update images or graphics, follow the nf-core [style guidelines](https:// - [ ] Keep the `[ meta, data ]` tuple shape across module and subworkflow boundaries, so sample metadata reaches every downstream step. - [ ] Put local subworkflows in `subworkflows/local//main.nf`. - [ ] Add a `CHANGELOG.md` entry with the PR number for every user-facing change. -- [ ] Tag fast (stub) tests with `small`: pull-request CI runs only tests with that tag. The extended pipeline tests (`clair_only`, `consensus`, `deep_only`, `union`) run only on release or manual dispatch, so regenerate their snapshots whenever an output changes. +- [ ] Tag fast (stub) tests with `small`: pull-request CI runs only tests with that tag. The extended pipeline tests (all tests tagged `extended`; currently `chm13`, `clair_only`, `consensus`, `deep_only` and `union`) run only on release or manual dispatch, so regenerate their snapshots whenever an output changes. diff --git a/nextflow.config b/nextflow.config index adc6b318..e0c36209 100644 --- a/nextflow.config +++ b/nextflow.config @@ -128,7 +128,7 @@ params { save_secondary_alignment = true // Fibertools options - autocorrelation = null + autocorrelation = false // Severus options severus_minsupport = 3 diff --git a/nextflow_schema.json b/nextflow_schema.json index 893a4690..a3955b6c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -225,8 +225,9 @@ "default": "", "properties": { "autocorrelation": { - "type": "string", - "description": "Pass --acf to fibertools qc to add the nucleosome autocorrelation to the Fiber-seq QC output. Any non-empty value turns it on." + "type": "boolean", + "default": false, + "description": "Pass --acf to fibertools qc to add nucleosome autocorrelation to the Fiber-seq QC output." } } }, From bd5dace2e575c8bf43ecc5c6d3fde6ab1d7d3bfd Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Mon, 2 Nov 2026 16:24:52 +0100 Subject: [PATCH 08/10] CLAIR3: decide GPU mode from params.use_gpu task.accelerator could disagree with params.use_gpu, which still picks CLAIR3's label and container, whenever a config set accelerator on its own: GPU flags on the CPU image, or CPU mode on the GPU image. Read the param, as DeepVariant, DeepSomatic and fibertools do. Addresses the #224 review. Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 2 +- modules/local/clair3/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0cc8011b..b4b05952 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,7 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, sets `manifest.diagram` to the existing metro map (`assets/lrsomatic_1.0.png`), replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). -- [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). +- [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template. `CLAIR3` now reads `params.use_gpu` instead of `task.ext.use_gpu`, the same param that picks its label and container, as DeepVariant, DeepSomatic and fibertools already do (@ljwharbers). - [#204](https://github.com/IntGenomicsLab/lrsomatic/pull/204) - With `--modkit_phased` set and haplotype DMR running, `5hmC` is appended to `--modified-bases` whenever `--modkit_args` names `5mC` without it, so the published `modkit_pileup/*_{hp1,hp2,combined}.bed.gz` now carry a 5hmC row next to each 5mC row. `modkit dmr pair` rejects bedMethyl rows whose valid coverage includes uncounted (`N_other`) calls, which ONT SUP data calling both 5mC and 5hmC produces under the `--cpg --modified-bases 5mC` default. Runs with `--skip_dmr`, without `--modkit_phased`, or without DMR references keep `--modkit_args` exactly as given (@YannVRB). - [#205](https://github.com/IntGenomicsLab/lrsomatic/pull/205) - Moved the fiber-seq steps into a `FIBERSEQ` subworkflow and the AmpliconArchitect MD5 default into `aaDataRepoMd5()`, because with dev merged the `LRSOMATIC` workflow body exceeded the 65,535-character limit on a compiled string and failed to compile; behaviour is unchanged (@robert-a-forsyth). - [#205](https://github.com/IntGenomicsLab/lrsomatic/pull/205) - `--download_sigprofiler_genome` now defaults to `true`, so a run without `--sigprofiler_genome_dir` installs the SigProfiler genome instead of stopping at launch; a given directory still wins (@robert-a-forsyth). diff --git a/modules/local/clair3/main.nf b/modules/local/clair3/main.nf index 6611f062..030df600 100644 --- a/modules/local/clair3/main.nf +++ b/modules/local/clair3/main.nf @@ -26,7 +26,7 @@ process CLAIR3 { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" - def use_gpu = task.accelerator?.request as boolean + def use_gpu = params.use_gpu as boolean // An empty model input means the model is bundled with the image: models/ next to run_clair3.sh // in the biocontainer, /opt/models in the HKU Docker image def model_path = model ? "${model}" : "\${CLAIR3_MODELS}/${meta.clair3_model}" From f1066e48cf72c8b3cc10fe13cdffbe0bb58f236b Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Mon, 2 Nov 2026 16:45:54 +0100 Subject: [PATCH 09/10] CLAIR3: GPU image v2.0.2_gpu -> v2.0.5_gpu With --use_gpu, Clair3 2.0.2 aborted at start with "Reference index fai file not found": run_clair3.py resolve()s a relative --ref_fn, following Nextflow's symlink into the FASTA's own task dir, and the .fai is staged from a different task. 2.0.3+ uses absolute() instead. v2.0.5_gpu has that fix and bundles the same models as before; CPU runs keep the 2.0.3 biocontainer. Found by a --use_gpu test run for the #224 review. Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 13 +++++++------ modules/local/clair3/main.nf | 7 ++++--- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b4b05952..18b3ef2d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -63,6 +63,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Fixed `CLAIR3` with `--use_gpu`, which failed at start with "Reference index fai file not found". The GPU image `hkubal/clair3:v2.0.2_gpu` follows the reference symlink and looks for the `.fai` next to the real file, but Nextflow stages the index from a different task. The GPU image is now `hkubal/clair3:v2.0.5_gpu`, which has the fix and bundles the same models. CPU runs keep the 2.0.3 biocontainer (@ljwharbers). - [#223](https://github.com/IntGenomicsLab/lrsomatic/pull/223) - Fixed the Severus input channel (@robert-a-forsyth). - [#205](https://github.com/IntGenomicsLab/lrsomatic/pull/205) - `PREPARE_AA_DATA_REPO` no longer reads a `versions` output `UNTAR` does not have, which crashed every default GRCh38 run with CoRAL; overriding `--aa_data_repo_url` drops the genome's default MD5 (@robert-a-forsyth). - [#205](https://github.com/IntGenomicsLab/lrsomatic/pull/205) - `-profile test_full` starts again: it skips CoRAL and signatures and carries the chr19 SAVANA workarounds from `test` (@robert-a-forsyth). @@ -114,12 +115,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#213](https://github.com/IntGenomicsLab/lrsomatic/pull/213) - Updated the small variant callers. **Germline and somatic calls change** with the new models (@ljwharbers). - | Tool | Old | New | Notes | - | ------------- | ----- | ------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | - | `clair3` | 1.2.0 | 2.0.3 | Clair3 v2 runs on PyTorch and **cannot read the v1 TensorFlow models** the pipeline downloaded from ONT's CDN. Models bundled with the image (HKU's and ONT's recent R10.4.1 SUP/HAC ones, `hifi_revio`) are now used from the image with no download; other models are fetched as PyTorch directories from HKU (ONT's Rerio catalogue for `r9`/`r10` names) by the new `CLAIR3_MODEL` step, which replaces `WGET`/`UNTAR` and, unlike `WGET`, checks the TLS certificate (Clair3 unpickles the files). The GPU image is `hkubal/clair3:v2.0.2_gpu`, the newest published | - | `clairs` | 0.4.4 | 0.5.1 | Bundles Clair3 2.0.3 for its germline step | - | `deepvariant` | 1.9.0 | 1.10.0 | nf-core update; `make_examples` now takes its flags from the model (`--checkpoint`): the ONT model is 199 wide with the new fuzzy channel, and both models call easy sites with the small model | - | `deepsomatic` | 1.7.0 | 1.10.0 | `make_examples_somatic` now takes its flags from the model (`--checkpoint`) instead of a hard-coded channel list and pileup width; the paired PacBio model is 147 wide with 9 channels. The small model is kept off explicitly (`--nocall_small_model_examples`), because the module does not pass its calls on | + | Tool | Old | New | Notes | + | ------------- | ----- | ------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | + | `clair3` | 1.2.0 | 2.0.3 | Clair3 v2 runs on PyTorch and **cannot read the v1 TensorFlow models** the pipeline downloaded from ONT's CDN. Models bundled with the image (HKU's and ONT's recent R10.4.1 SUP/HAC ones, `hifi_revio`) are now used from the image with no download; other models are fetched as PyTorch directories from HKU (ONT's Rerio catalogue for `r9`/`r10` names) by the new `CLAIR3_MODEL` step, which replaces `WGET`/`UNTAR` and, unlike `WGET`, checks the TLS certificate (Clair3 unpickles the files). The GPU image is `hkubal/clair3:v2.0.5_gpu` (was `v2.0.2_gpu` until #224; see Fixed) | + | `clairs` | 0.4.4 | 0.5.1 | Bundles Clair3 2.0.3 for its germline step | + | `deepvariant` | 1.9.0 | 1.10.0 | nf-core update; `make_examples` now takes its flags from the model (`--checkpoint`): the ONT model is 199 wide with the new fuzzy channel, and both models call easy sites with the small model | + | `deepsomatic` | 1.7.0 | 1.10.0 | `make_examples_somatic` now takes its flags from the model (`--checkpoint`) instead of a hard-coded channel list and pileup width; the paired PacBio model is 147 wide with 9 channels. The small model is kept off explicitly (`--nocall_small_model_examples`), because the module does not pass its calls on | - [#214](https://github.com/IntGenomicsLab/lrsomatic/pull/214) - Updated Wakhan from 0.4.4 to 0.5.0, run from `docker.io/ljwharbers/wakhan:0.5.0-histfix-1afd44d` (`oras://docker.io/ljwharbers/wakhan-sif:0.5.0-histfix-1afd44d` for Singularity/Apptainer) because no biocontainer was built for it. The image carries upstream commit 1afd44d4, which fixes the `IndexError` in `update_coverage_hist` that killed WAKHAN on some samples (KolmogorovLab/Wakhan#64). **The `wakhan/` output layout changes**: each solution is now `solution_{ploidy}_{purity}_{confidence}/` with `integer_profile.{bed,vcf,html,pdf}` (one boundary-aligned table for both haplotypes, replacing the two `*_HP_{1,2}.bed` files), `subclonal_profile.*`, `genes/genes_copynumber_states.*` and a `HiScanner_plots_data.zip` for the Wakhan web viewer; ranked solutions are `solution_rank_{n}`. Wakhan 0.5.0 no longer writes the per-chromosome `variation_plots`, `genome_copynumbers_details` plots or per-solution `loh_regions*.bed`. `LRSOMATICREPORT` now runs lrsomatic_report v1.6.1 (`ghcr.io/ljwharbers/lrsomatic-report:1.6.1`), which finds the copy-number plots in both layouts; v1.6.0 silently dropped them for 0.5.0 output. The WAKHAN stub now writes the outputs the module declares, and the version comes from `wakhan --version` (@ljwharbers). diff --git a/modules/local/clair3/main.nf b/modules/local/clair3/main.nf index 030df600..fd09cd7c 100644 --- a/modules/local/clair3/main.nf +++ b/modules/local/clair3/main.nf @@ -3,10 +3,11 @@ process CLAIR3 { label "${params.use_gpu ? 'process_gpu_very_high' : 'process_very_high'}" conda "${moduleDir}/environment.yml" - // No GPU image was published for 2.0.3; 2.0.2 differs only by the --gender option, which is not used here + // GPU: HKU's image (no biocontainer has CUDA). Needs >= 2.0.3: 2.0.2 resolves the reference symlink and then + // misses the .fai, which Nextflow stages from a different task. Bundles the same models as the biocontainer. container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? - (params.use_gpu ? 'docker://docker.io/hkubal/clair3:v2.0.2_gpu' : 'https://depot.galaxyproject.org/singularity/clair3:2.0.3--py311hbc58adc_0') : - (params.use_gpu ? 'docker.io/hkubal/clair3:v2.0.2_gpu' : 'quay.io/biocontainers/clair3:2.0.3--py311hbc58adc_0') }" + (params.use_gpu ? 'docker://docker.io/hkubal/clair3:v2.0.5_gpu' : 'https://depot.galaxyproject.org/singularity/clair3:2.0.3--py311hbc58adc_0') : + (params.use_gpu ? 'docker.io/hkubal/clair3:v2.0.5_gpu' : 'quay.io/biocontainers/clair3:2.0.3--py311hbc58adc_0') }" input: tuple val(meta) , path(bam), path(bai), path(model), val(platform) From 0c1cf3f3905b34ab373efde2a0fa1e1b66aa50f3 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Mon, 2 Nov 2026 17:13:10 +0100 Subject: [PATCH 10/10] Document --use_gpu: every affected tool and the Clair3 GPU limit docs/usage.md named only DeepVariant and DeepSomatic, but Clair3 and the fibertools GPU steps switch on the same param. Also note the gpu profile and that hkubal/clair3:v2.0.5_gpu supports compute capability <= 9.0, so it fails on B200s. Addresses the #224 re-review. Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 2 +- docs/usage.md | 8 ++++---- nextflow_schema.json | 3 ++- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 18b3ef2d..5a5b86b1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -63,7 +63,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Fixed `CLAIR3` with `--use_gpu`, which failed at start with "Reference index fai file not found". The GPU image `hkubal/clair3:v2.0.2_gpu` follows the reference symlink and looks for the `.fai` next to the real file, but Nextflow stages the index from a different task. The GPU image is now `hkubal/clair3:v2.0.5_gpu`, which has the fix and bundles the same models. CPU runs keep the 2.0.3 biocontainer (@ljwharbers). +- [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Fixed `CLAIR3` with `--use_gpu`, which failed at start with "Reference index fai file not found". The GPU image `hkubal/clair3:v2.0.2_gpu` follows the reference symlink and looks for the `.fai` next to the real file, but Nextflow stages the index from a different task. The GPU image is now `hkubal/clair3:v2.0.5_gpu`, which has the fix and bundles the same models. CPU runs keep the 2.0.3 biocontainer. The image doesn't run on GPUs newer than compute capability 9.0, such as the B200. `docs/usage.md` and the schema now say so and list every tool that `--use_gpu` affects (@ljwharbers). - [#223](https://github.com/IntGenomicsLab/lrsomatic/pull/223) - Fixed the Severus input channel (@robert-a-forsyth). - [#205](https://github.com/IntGenomicsLab/lrsomatic/pull/205) - `PREPARE_AA_DATA_REPO` no longer reads a `versions` output `UNTAR` does not have, which crashed every default GRCh38 run with CoRAL; overriding `--aa_data_repo_url` drops the genome's default MD5 (@robert-a-forsyth). - [#205](https://github.com/IntGenomicsLab/lrsomatic/pull/205) - `-profile test_full` starts again: it skips CoRAL and signatures and carries the chr19 SAVANA workarounds from `test` (@robert-a-forsyth). diff --git a/docs/usage.md b/docs/usage.md index 044e9e02..7a07bd77 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -580,10 +580,10 @@ lost: they remain in `variants/phased/germline_smallvariants.vcf.gz`, in #### Advanced Options -| Parameter | Description | -| ----------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `--use_gpu` | A boolean to enable GPU acceleration for DeepVariant and DeepSomatic. Requires a GPU-enabled compute environment. Default = `false` | -| `--generate_gvcf` | A boolean to enable gVCF output from DeepVariant (germline) and DeepSomatic (somatic). gVCF files include calls at all positions, not just variant sites. Default = `false` | +| Parameter | Description | +| ----------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `--use_gpu` | A boolean to run DeepVariant, DeepSomatic, Clair3 and the fibertools steps (m6A prediction, nucleosomes, FIRE) on a GPU, with their GPU container images. Needs a GPU-enabled compute environment; add the `gpu` profile (`-profile <...>,gpu`) so the containers can see the GPU. Clair3's GPU image (`hkubal/clair3:v2.0.5_gpu`) is built for NVIDIA GPUs up to compute capability 9.0 (for example A100, H100 or RTX Ada) and fails on newer cards such as the B200; there, leave `--use_gpu` off. Default = `false` | +| `--generate_gvcf` | A boolean to enable gVCF output from DeepVariant (germline) and DeepSomatic (somatic). gVCF files include calls at all positions, not just variant sites. Default = `false` | #### Genome-Derived Parameters diff --git a/nextflow_schema.json b/nextflow_schema.json index 04f31ded..667eceee 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -732,7 +732,8 @@ }, "use_gpu": { "type": "boolean", - "description": "Use GPU for supported tools (e.g. DeepVariant, DeepSomatic, Clair3)" + "description": "Run DeepVariant, DeepSomatic, Clair3 and fibertools on a GPU (use with the gpu profile).", + "help_text": "Clair3's GPU image supports NVIDIA GPUs up to compute capability 9.0 (A100, H100, RTX Ada); it fails on newer cards such as the B200, so leave this off there." }, "skip_report": { "type": "boolean",