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chore(nfcore_build): bump nf-core/tools to 4.1.0 - #1014

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FriederikeHanssen merged 3 commits into
fix/nfcore-build-training-fixesfrom
bump/nfcore-build-tools-4.1.0
Oct 14, 2026
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chore(nfcore_build): bump nf-core/tools to 4.1.0#1014
FriederikeHanssen merged 3 commits into
fix/nfcore-build-training-fixesfrom
bump/nfcore-build-tools-4.1.0

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@FriederikeHanssen

@FriederikeHanssen FriederikeHanssen commented Oct 14, 2026 •
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Stacked on #1012. This bumps nf-core/tools in the Hello nf-core course (nfcore_build) from 4.0.2 to 4.1.0.

It contains only the changes 4.1.0 requires. There are no style or wording edits. Each part was walked through with nf-core/tools 4.1.0 and Nextflow 26.04.4, and every change below was checked against this branch.

Changes

  • .devcontainer/local-features/uv-tools/install.sh: nf-core==4.1.0
  • 00_orientation.md: the required version is now 4.1.0
  • Parts 1, 2 and 4: the nf-core/tools version banner in command output
  • Part 1 §2.1: nf-core pipelines create no longer prints Generated container configs for the pipeline successfully. (the template has no modules/ yet). Removed that line and the matching words in the sentence before it.
  • Part 1 §5.1–5.2: in the 4.1.0 template the input-channel block in utils_nfcore_hello_pipeline/main.nf starts at line 84, not 83. Updated linenums. The content is unchanged.
  • Part 2 §1.3: the note about the modules info "Reinstalling modules…" message now gives 4.1.0 as the version. The message still appears.
  • Part 2 §1.4: nf-core modules install find/concatenate no longer fails with NotADirectoryError on the single-file cowpy.nf local module. It exits cleanly and prints the include statement. Replaced the output block and removed the paragraph about the traceback.

Solutions (nfcore-build/solutions/core-hello-part1 to part4)

These were 4.0.2 scaffolds. I applied the exact 4.0.2 → 4.1.0 template diff, taken from nf-core pipelines create run with both versions:

  • subworkflows/nf-core/utils_nfschema_plugin/: the 4.1.0 version, with the new cli_typecast input and the parameters_schema option keys. tests/nextflow.config keeps fix(nfcore_build): correct Build with nf-core materials for the training environment #1012's nf-schema 2.7.2.
  • subworkflows/local/utils_nfcore_hello_pipeline/main.nf: passes the extra false argument to UTILS_NFSCHEMA_PLUGIN.
  • conf/base.config: the new process_low_memory label.
  • modules.json: new SHAs for utils_nextflow_pipeline and utils_nfschema_plugin.
  • .nf-core.yml: nf_core_version: 4.1.0.
  • docs/output.md and docs/usage.md: template wording.

Docs that show these files:

  • Part 2 §1.4: the modules.json block uses the new SHAs.
  • Part 4 §2.5: the line numbers for utils_nfcore_hello_pipeline/main.nf change from 83 to 84.
  • Part 4 §1.5 and §2.7.2: the validation error now reports utils_nfschema_plugin/main.nf' at line: 72. It was line 68.

Verification

  • Parts 2, 3 and 4 were walked through again on this branch with the updated solutions, using nf-core/tools 4.1.0 and Nextflow 26.04.4.
  • core-hello-part1 to part4 all pass a fresh run and a -resume run with -profile docker,test.
  • nf-schema 2.7.2 accepts cast_cli_params: false. The validation messages are otherwise unchanged.

Not changed

  • Part 3: the module template is byte-identical in 4.0.2 and 4.1.0. The walkthrough found nothing caused by 4.1.0.
  • Part 4: schema build output and validation errors are unchanged.
  • The 4.1.0 template still pins nf-schema 2.5.1, so the step in fix(nfcore_build): correct Build with nf-core materials for the training environment #1012 that switches to 2.7.2 is still needed.
  • Part 2 modules.json formatting: 4.1.0 runs prettier on modules.json only when the pipeline is inside a git repo. Outside one, the output matches the current block. Inside one, the arrays are written on one line with 2-space indentation. I left the block as it is because this depends on the environment.
  • Translations are not updated.

🤖 Generated with Claude Code

@FriederikeHanssen @claude
chore(nfcore_build): bump nf-core/tools to 4.1.0
295581a 
Update the devcontainer pin, the required-version text in the
orientation page, and the nf-core/tools banners in lesson output.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@github-actions

github-actions Bot commented Oct 14, 2026 •
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Nextflow linting complete!

❌ 1 files had 5 errors
⚠️ 19 files had 29 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 34 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: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: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/local/cowpy/main.nf:30:9 Variable was declared but not used
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: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/local/cowpy/main.nf:30:9 Variable was declared but not used
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: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)
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FriederikeHanssen and others added 2 commits October 14, 2026 11:08
@FriederikeHanssen @claude
fix(nfcore_build): update command output and line numbers for nf-core…
5979be0 
…/tools 4.1.0

- Part 1 §2.1: pipelines create no longer prints the container-config line
- Part 1 §5.1-5.2: input-channel block starts at line 84 in the 4.1.0 template
- Part 2 §1.4: modules install no longer fails with NotADirectoryError on
  single-file local modules; it now prints the include statement

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@FriederikeHanssen @claude
fix(nfcore_build): update solutions to the nf-core/tools 4.1.0 template
92ac244 
Apply the 4.0.2 -> 4.1.0 template changes to core-hello-part1..4:
updated utils_nfschema_plugin subworkflow (cli_typecast input,
parameters_schema option keys), the extra argument passed to it from the
local utils subworkflow, the process_low_memory label, new subworkflow
SHAs in modules.json, and nf_core_version in .nf-core.yml.

Update the docs that show these files: the modules.json SHAs in Part 2,
and the utils_nfcore_hello_pipeline line numbers and the
utils_nfschema_plugin error line in Part 4.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@FriederikeHanssen
FriederikeHanssen marked this pull request as ready for review October 14, 2026 09:49
@FriederikeHanssen
FriederikeHanssen merged commit d47df77 into fix/nfcore-build-training-fixes Oct 14, 2026
6 checks passed
@FriederikeHanssen
FriederikeHanssen deleted the bump/nfcore-build-tools-4.1.0 branch October 14, 2026 09:49
pinin4fjords added a commit that referenced this pull request Oct 14, 2026
@pinin4fjords @FriederikeHanssen @claude
fix(nfcore_build): correct Build with nf-core materials for the train…
564dba7 
…ing environment (#1012)

* fix(nfcore_build): correct Hello nf-core materials for the training environment

Fix bugs and inaccuracies in the Build with nf-core course against the
training image (Nextflow 26.04.4, nf-core/tools 4.0.2), found in Friederike's
walkthrough (#1005-#1011) and re-verified on 4.0.2:

- Demo symlink: Nextflow 26.04 stores pulled pipelines under
  assets/.repos/<org>/<name>/clones/<commit>, so the old assets symlink
  left pipelines/nf-core/demo missing.
- nf-core/demo now ships modules/local/cowpy; update the modules tree.
- Line numbers, highlights and Before blocks that did not match the files
  produced by the 4.0.2 template and the lesson steps.
- modules create: tool name must be lowercase, document the Bioconda
  prompt, and show the generated main.nf as 4.0.2 writes it.
- find/concatenate excerpt now matches the installed module signature.
- Part 4: declare batch in nextflow.config before schema build, and pass
  --batch in the invalid-input test so the output shows only file errors.
- Solutions: part4 validate_params = true, composable-hello docker config,
  and FIND_CONCATENATE include order matching Part 2.

Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix(nfcore_build): align solutions with lesson end state and document install traceback

- Solutions part1-4: workflows/hello.nf and the utils_nfcore_hello_pipeline
  subworkflow now match what the 4.0.2 template plus the lesson edits
  produce, so the "start fresh" boxes give files that match the Before
  blocks and line numbers.
- Part 2: show the long traceback that `nf-core modules install` prints
  before NotADirectoryError on 4.0.2, and drop the claim that `info`
  writes no files (it rewrites modules.json).

Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix(nfcore_build): have attendees switch their scaffold to nf-schema 2.7.2

The nf-core/tools pipeline template pins nf-schema 2.5.1, which prints
`WARN: Unrecognized config option 'validation.*'` on every run under
Nextflow 26.04. The solutions and the Part 2-4 docs are written against
2.7.2, but nothing told attendees to switch, so their runs never matched
the documented output. Part 1 §2.2 now has them update the pin, the
§5.5 output shows the one-off plugin download, and the stray download
line in Part 3 §1.2.4 is removed.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix(nfcore_build): clone nf-core/demo for browsing instead of symlinking the asset cache

`nextflow clone` puts the default revision directly at pipelines/nf-core/demo,
so the setup no longer depends on the Nextflow 26.04 per-revision clone
layout. The course only reads the demo code, so the pull is not needed.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* docs(nfcore_build): point Part 1 file-explorer instruction at pipelines/nf-core/demo

Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* chore(nfcore_build): bump nf-core/tools to 4.1.0 (#1014)

* chore(nfcore_build): bump nf-core/tools to 4.1.0

Update the devcontainer pin, the required-version text in the
orientation page, and the nf-core/tools banners in lesson output.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

* fix(nfcore_build): update command output and line numbers for nf-core/tools 4.1.0

- Part 1 §2.1: pipelines create no longer prints the container-config line
- Part 1 §5.1-5.2: input-channel block starts at line 84 in the 4.1.0 template
- Part 2 §1.4: modules install no longer fails with NotADirectoryError on
  single-file local modules; it now prints the include statement

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

* fix(nfcore_build): update solutions to the nf-core/tools 4.1.0 template

Apply the 4.0.2 -> 4.1.0 template changes to core-hello-part1..4:
updated utils_nfschema_plugin subworkflow (cli_typecast input,
parameters_schema option keys), the extra argument passed to it from the
local utils subworkflow, the process_low_memory label, new subworkflow
SHAs in modules.json, and nf_core_version in .nf-core.yml.

Update the docs that show these files: the modules.json SHAs in Part 2,
and the utils_nfcore_hello_pipeline line numbers and the
utils_nfschema_plugin error line in Part 4.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
@FriederikeHanssen FriederikeHanssen mentioned this pull request Oct 14, 2026
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@FriederikeHanssen @pinin4fjords