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fix(nfcore_build): update to nf-core/tools 4.1.0 and current nf-core/demo - #1008

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fix/nfcore-build-batch-paramfrom
fix/nfcore-build-tools-drift
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fix(nfcore_build): update to nf-core/tools 4.1.0 and current nf-core/demo#1008
FriederikeHanssen wants to merge 2 commits into
fix/nfcore-build-batch-paramfrom
fix/nfcore-build-tools-drift

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@FriederikeHanssen

@FriederikeHanssen FriederikeHanssen commented Oct 13, 2026

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Summary

The Hello nf-core course's documented tool output no longer matched nf-core/tools 4.1.0 or the current nf-core/demo pipeline. This PR updates the docs and solutions to match, and bumps the devcontainer pin from nf-core==4.0.2 to 4.1.0 in the same change. Docs and environment have to move together: on 4.0.2 the old text was correct (for example, modules install still raises NotADirectoryError).

Stacked on #1007 (→ #1006 → #1005). Review only the 2 commits in this PR.

Changes

Location Change
.devcontainer/local-features/uv-tools/install.sh nf-core==4.0.2 → 4.1.0. Only nf-core is installed by this script, and it's also what the ghcr.io/nextflow-io/training image build uses. No CI job runs nf-core commands.
nfcore_build/00_orientation.md, nfcore_use/00_orientation.md Version text 4.0.2 → 4.1.0
01 §1 demo tree nf-core/demo 1.2.0 now ships modules/local/cowpy. Updated the tree and replaced "there are no local modules" with a short local vs nf-core modules explanation.
01 §2.1 create output 4.1.0 banner. Removed Generated container configs…, which 4.1.0 doesn't print without a modules/ directory.
01 §5.1/5.2 Template excerpt now shows samplesheetToList(input, …) at line 84 (fresh 4.1.0 template), plus a note on where input comes from.
01 §5.5 output Adds the two WARN: Unrecognized config option 'validation.*' lines a fresh-template run prints
02 §1.3-1.4 Install output matches 4.1.0 (prints the include statement, no NotADirectoryError). Removed the "ignore the error" paragraph. "Reinstalling modules…" prose no longer names a version. Dropped the cd core-hello that failed for learners who used the start-fresh box.
02 §2 excerpts Input line now shows the real path(files_in, stageAs: 'to_concatenate/*', arity: '1..*'), with one sentence explaining it
03 §2 modules create uses lowercase cowpy (4.1.0 warns on COWPY). Documents the new Bioconda prompt. Generated main.nf blocks match the 4.1.0 template: leading blank lines, one-line input:, corrected linenums/hl_lines. Removed the unused def args from the stub (nextflow lint: Variable was declared but not used).
Solutions part1-4 .nf-core.yml nf_core_version: 4.1.0. workflows/hello.nf uses def ch_versions = … / def ch_collated_versions = …, as in the docs and the 4.1.0 template. cowpy stub args removed in part3/4.

Testing

Run with nf-core/tools 4.1.0, Nextflow 26.04.4, the v2 parser and Docker. An independent second pass re-reproduced each claim.

  • Every changed output block comes from a real run. Banner, pipelines create, modules install, modules create (prompts driven through a pty) and the §5.5 run all checked.
  • Applying the 03 §2.2-2.3 Before/After blocks in order to the freshly generated main.nf reproduces solutions/core-hello-part3/modules/local/cowpy/main.nf
  • Solutions part1-4 run with -profile test,docker and print Pipeline completed successfully. nextflow lint shows no errors.
  • Checked the bump with 4.0.2 vs 4.1.0 side by side: no other course runs nf-core commands. nf-schema stays at 2.5.1 and nextflowVersion is unchanged.
  • check_headings, /check-highlights and pre-commit pass

Not in this PR

  • docs/en/docs/nfcore_build/img/nf-core_demo_code_organization.svg doesn't show the new local/cowpy module and needs a manual diagram update.
  • Translations (11 languages) still say 4.0.2 and need regenerating after this series lands.
  • A Part 1 pipeline created with 4.1.0 differs slightly from solutions/core-hello-part1, which was made with 4.0.2 (extra cli_typecast input to UTILS_NFSCHEMA_PLUGIN, process_low_memory label). The lesson code doesn't depend on either.

🤖 Generated with Claude Code

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github-actions Bot commented Oct 13, 2026 •
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Nextflow linting complete!

❌ 1 files had 5 errors
⚠️ 19 files had 31 warnings
✅ 183 files had no errors
🔧 130 files would be changed by auto-formatting

💡 Tip: Click filename locations to go directly to that code.

View all 36 issues
Type Location Message
Error hello-nextflow/solutions/6-hello-config/hello-config.nf:44:16 sayHello is not defined
Error hello-nextflow/solutions/6-hello-config/hello-config.nf:47:16 convertToUpper is not defined
Error hello-nextflow/solutions/6-hello-config/hello-config.nf:50:16 collectGreetings is not defined
Error hello-nextflow/solutions/6-hello-config/hello-config.nf:53:16 collectGreetings is not defined
Error hello-nextflow/solutions/6-hello-config/hello-config.nf:56:16 cowpy is not defined
Warning nfcore-build/solutions/core-hello-part1/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part1/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part1/workflows/hello.nf:61:9 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-part2/modules/nf-core/find/concatenate/main.nf:19:5 The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime
Warning nfcore-build/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part2/workflows/hello.nf:45:55 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part2/workflows/hello.nf:70:9 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-part3/modules/local/cowpy/main.nf:17:5 The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime
Warning nfcore-build/solutions/core-hello-part3/modules/nf-core/find/concatenate/main.nf:19:5 The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime
Warning nfcore-build/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part3/workflows/hello.nf:67:9 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-part4/modules/local/cowpy/main.nf:17:5 The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime
Warning nfcore-build/solutions/core-hello-part4/modules/nf-core/find/concatenate/main.nf:19:5 The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime
Warning nfcore-build/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part4/workflows/hello.nf:67:9 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-start/workflows/hello.nf:18:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-start/workflows/hello.nf:45:9 Variable was declared but not used
Warning side-quests/solutions/debugging/buggy_workflow.nf:91:44 Implicit closure parameter is deprecated, declare an explicit parameter instead
Warning side-quests/solutions/essential_scripting_patterns/main.nf:59:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/essential_scripting_patterns/main.nf:63:53 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/essential_scripting_patterns/main.nf:68:5 Variable was declared but not used
Warning side-quests/solutions/essential_scripting_patterns/main.nf:69:5 Variable was declared but not used
Warning side-quests/solutions/metadata/1.2/main.nf:5:5 Variable was declared but not used
Warning side-quests/solutions/splitting_and_grouping/main.nf:11:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/splitting_and_grouping/main.nf:14:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/splitting_and_grouping/main.nf:29:5 Variable was declared but not used
Warning side-quests/solutions/working_with_files/6/main.nf:10:43 Variable was declared but not used
Warning side-quests/solutions/working_with_files/6/main.nf:30:22 Parameter was not used -- prefix with _ to suppress warning
View formatting changes
FileDiff
hello-nextflow/solutions/1-hello-world/hello-world-2.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     output:
     path 'output.txt'
hello-nextflow/solutions/1-hello-world/hello-world-3.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -29,7 +28,7 @@ workflow {
     main:
     // create a channel for inputs
     greeting_ch = channel.of('Hello Channels!')
-                        .view()
+        .view()
     // emit a greeting
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -29,7 +28,7 @@ workflow {
     main:
     // create a channel for inputs
     greeting_ch = channel.of('Hello', 'Bonjour', 'Hola')
-                        .view()
+        .view()
     // emit a greeting
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -28,12 +27,12 @@ workflow {
 
     main:
     // declare an array of input greetings
-    greetings_array = ['Hello','Bonjour','Hola']
+    greetings_array = ['Hello', 'Bonjour', 'Hola']
     // create a channel for inputs
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -29,11 +28,11 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .view { csv -> "Before splitCsv: $csv" }
-                        .splitCsv()
-                        .view { csv -> "After splitCsv: $csv" }
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf
View 
@@ -7,7 +7,6 @@ include { sayHello } from './modules/sayHello.nf'
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
 
@@ -24,7 +23,6 @@ process convertToUpper {
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf
View 
@@ -8,7 +8,6 @@ include { convertToUpper } from './modules/convertToUpper.nf'
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
@@ -38,8 +37,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf
View 
@@ -18,8 +18,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
     // emit a greeting
     sayHello(greeting_ch)
     // convert the greeting to uppercase
hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf
View 
@@ -2,7 +2,6 @@
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf
View 
@@ -2,7 +2,6 @@
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf
View 
@@ -2,7 +2,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf
View 
@@ -20,8 +20,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
     // emit a greeting
     sayHello(greeting_ch)
     // convert the greeting to uppercase
hello-nextflow/solutions/5-hello-containers/modules/collectGreetings.nf
View 
@@ -2,7 +2,6 @@
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
hello-nextflow/solutions/5-hello-containers/modules/convertToUpper.nf
View 
@@ -2,7 +2,6 @@
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
hello-nextflow/solutions/5-hello-containers/modules/sayHello.nf
View 
@@ -2,7 +2,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/6-hello-config/modules/collectGreetings.nf
View 
@@ -2,7 +2,6 @@
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
hello-nextflow/solutions/6-hello-config/modules/convertToUpper.nf
View 
@@ -2,7 +2,6 @@
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
hello-nextflow/solutions/6-hello-config/modules/sayHello.nf
View 
@@ -2,7 +2,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/6-hello-config/nextflow.config
View 
@@ -2,19 +2,19 @@ docker.enabled = false
 conda.enabled = true
 
 /*
-* Process settings
-*/
+ * Process settings
+ */
 process {
     memory = 1.GB
-    withName: 'cowpy' {
+    withName: cowpy {
         memory = 2.GB
         cpus = 2
     }
... (truncated)
nfcore-build/solutions/composable-hello/hello.nf
View 
@@ -14,7 +14,6 @@ include { collectGreetings } from './modules/collectGreetings.nf'
 include { cowpy } from './modules/cowpy.nf'
 
 workflow HELLO {
-
     take:
     // channel of greetings
     greeting_ch
nfcore-build/solutions/composable-hello/main.nf
View 
@@ -9,12 +9,12 @@ params.greeting = 'greetings.csv'
 workflow {
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.greeting)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
 
     // call the imported workflow on the channel of greetings
     HELLO(greeting_ch)
 
     // view the outputs emitted by the workflow
-    HELLO.out.view { output -> "Output: $output" }
+    HELLO.out.view { output -> "Output: ${output}" }
... (truncated)
nfcore-build/solutions/composable-hello/modules/collectGreetings.nf
View 
@@ -10,8 +10,8 @@ process collectGreetings {
     val batch_name
 
     output:
-    path "COLLECTED-${batch_name}-output.txt" , emit: outfile
-    val count_greetings , emit: count
+    path "COLLECTED-${batch_name}-output.txt", emit: outfile
+    val count_greetings, emit: count
 
     script:
     count_greetings = input_files.size()
nfcore-build/solutions/composable-hello/modules/convertToUpper.nf
View 
@@ -13,6 +13,6 @@ process convertToUpper {
 
     script:
     """
-    cat $input_file | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
+    cat ${input_file} | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
     """
 }
nfcore-build/solutions/composable-hello/modules/cowpy.nf
View 
@@ -15,6 +15,6 @@ process cowpy {
 
     script:
     """
-    cat $input_file | cowpy -c "$character" > cowpy-${input_file}
+    cat ${input_file} | cowpy -c "${character}" > cowpy-${input_file}
     """
 }
nfcore-build/solutions/composable-hello/modules/sayHello.nf
View 
@@ -13,6 +13,6 @@ process sayHello {
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
     """
 }
nfcore-build/solutions/core-hello-part1/conf/base.config
View 
@@ -1,23 +1,23 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    core/hello Nextflow base config file
+core/hello Nextflow base config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    A 'blank slate' config file, appropriate for general use on most high performance
-    compute environments. Assumes that all software is installed and available on
-    the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.
+A 'blank slate' config file, appropriate for general use on most high performance
+compute environments. Assumes that all software is installed and available on
+the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.
 ----------------------------------------------------------------------------------------
-*/
+ */
... (truncated)
nfcore-build/solutions/core-hello-part1/conf/modules.config
View 
@@ -1,21 +1,16 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
+Config file for defining DSL2 per module options and publishing paths
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
+Available keys to override module options:
+ext.args   = Additional arguments appended to command in module.
+ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
... (truncated)
nfcore-build/solutions/core-hello-part1/conf/test.config
View 
@@ -1,31 +1,27 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
+Nextflow config file for running minimal tests
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines input files and everything required to run a fast and simple pipeline test.
+Defines input files and everything required to run a fast and simple pipeline test.
 
-    Use as follows:
-        nextflow run core/hello -profile test,<docker/singularity> --outdir <OUTDIR>
+Use as follows:
+nextflow run core/hello -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
... (truncated)
nfcore-build/solutions/core-hello-part1/conf/test_full.config
View 
@@ -1,17 +1,17 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running full-size tests
+Nextflow config file for running full-size tests
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines input files and everything required to run a full size pipeline test.
+Defines input files and everything required to run a full size pipeline test.
 
-    Use as follows:
-        nextflow run core/hello -profile test_full,<docker/singularity> --outdir <OUTDIR>
+Use as follows:
+nextflow run core/hello -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
... (truncated)
nfcore-build/solutions/core-hello-part1/main.nf
View 
@@ -1,32 +1,31 @@
 #!/usr/bin/env nextflow
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    core/hello
+core/hello
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Github : https://github.com/core/hello
+Github : https://github.com/core/hello
 ----------------------------------------------------------------------------------------
-*/
+ */
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
... (truncated)
nfcore-build/solutions/core-hello-part1/modules/local/collectGreetings.nf
View 
@@ -10,8 +10,8 @@ process collectGreetings {
     val batch_name
 
     output:
-    path "COLLECTED-${batch_name}-output.txt" , emit: outfile
-    val count_greetings , emit: count
+    path "COLLECTED-${batch_name}-output.txt", emit: outfile
+    val count_greetings, emit: count
 
     script:
     count_greetings = input_files.size()
nfcore-build/solutions/core-hello-part1/modules/local/convertToUpper.nf
View 
@@ -13,6 +13,6 @@ process convertToUpper {
 
     script:
     """
-    cat $input_file | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
+    cat ${input_file} | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
     """
 }
nfcore-build/solutions/core-hello-part1/modules/local/cowpy.nf
View 
@@ -7,14 +7,14 @@ process cowpy {
     conda 'conda-forge::cowpy==1.1.5'
 
     input:
-        path input_file
-        val character
+    path input_file
+    val character
 
     output:
-        path "cowpy-${input_file}"
+    path "cowpy-${input_file}"
 
     script:
     """
... (truncated)
nfcore-build/solutions/core-hello-part1/modules/local/sayHello.nf
View 
@@ -13,6 +13,6 @@ process sayHello {
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
     """
 }
nfcore-build/solutions/core-hello-part1/nextflow.config
View 
@@ -1,40 +1,40 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    core/hello Nextflow config file
+core/hello Nextflow config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Default config options for all compute environments
+Default config options for all compute environments
 ----------------------------------------------------------------------------------------
-*/
+ */
 
 // Global default params, used in configs
 params {
 
... (truncated)
nfcore-build/solutions/core-hello-part1/subworkflows/local/utils_nfcore_hello_pipeline/main.nf
View 
@@ -4,36 +4,35 @@
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
+IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+ */
 
-include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-schema'
-include { samplesheetToList         } from 'plugin/nf-schema'
-include { paramsHelp                } from 'plugin/nf-schema'
-include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
... (truncated)
nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
View 
@@ -4,15 +4,15 @@
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    SUBWORKFLOW DEFINITION
+SUBWORKFLOW DEFINITION
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+ */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
     take:
-    print_version        // boolean: print version
-    dump_parameters      // boolean: dump parameters
-    outdir               //    path: base directory used to publish pipeline results
... (truncated)
nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
View 
@@ -1,9 +1,9 @@
 manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
+    name = 'nextflow_workflow'
+    author = """nf-core"""
+    homePage = 'https://127.0.0.1'
+    description = """Dummy pipeline"""
     nextflowVersion = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+    version = '9.9.9'
+    doi = 'https://doi.org/10.5281/zenodo.5070524'
... (truncated)
nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nfcore_pipeline/main.nf(truncated)
nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
nfcore-build/solutions/core-hello-part1/workflows/hello.nf(truncated)
nfcore-build/solutions/core-hello-part2/conf/base.config(truncated)
nfcore-build/solutions/core-hello-part2/conf/modules.config(truncated)
nfcore-build/solutions/core-hello-part2/conf/test.config(truncated)
nfcore-build/solutions/core-hello-part2/conf/test_full.config(truncated)
nfcore-build/solutions/core-hello-part2/main.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/local/collectGreetings.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/local/convertToUpper.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/local/cowpy.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/local/sayHello.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/nf-core/find/concatenate/main.nf(truncated)
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This was referenced Oct 13, 2026
Closed
Closed
FriederikeHanssen and others added 2 commits October 13, 2026 15:21
@FriederikeHanssen @claude
fix(nfcore_build): align docs and solutions with nf-core/tools 4.1.0 …
7ee4a77 
…and nf-core/demo

- 01: show demo's local cowpy module, drop container-config log line,
  update samplesheetToList excerpt and linenums, add validation WARN lines
  to the test-profile run output
- 02: update modules install output, remove NotADirectoryError note,
  make install step work from either starting point, show real
  find/concatenate input declaration
- 03: use lowercase tool name for modules create, document Bioconda prompt,
  show real generated main.nf, drop unused args from stub
- solutions: use def for ch_versions/ch_collated_versions as in the
  template; drop unused args from cowpy stub

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@FriederikeHanssen @claude
Bump nf-core/tools to 4.1.0
3eab420 
Pin nf-core==4.1.0 in the devcontainer, update the English nfcore_build
and nfcore_use orientation pages and the schema-build banner in
04_input_validation, and set nf_core_version: 4.1.0 in the
core-hello-part1..4 solution .nf-core.yml files.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@FriederikeHanssen
FriederikeHanssen force-pushed the fix/nfcore-build-batch-param branch from 8fd4864 to bc21722 Compare October 13, 2026 13:21
@FriederikeHanssen
FriederikeHanssen force-pushed the fix/nfcore-build-tools-drift branch from 4dae36d to 3eab420 Compare October 13, 2026 13:21
@pinin4fjords

pinin4fjords commented Oct 13, 2026

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Superseded by #1012. Carried over: the demo local/cowpy tree, the samplesheetToList(input, ...) excerpt, def ch_collated_versions, the lowercase modules create cowpy and Bioconda prompt, the generated main.nf, the stageAs/arity signature, and the cd core-hello fix. These turned out to apply to 4.0.2 too. Not carried over: the bump to nf-core/tools 4.1.0 and the 4.1.0-only output, because the training runs on the 4.0.2 image.

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@FriederikeHanssen @pinin4fjords