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Migrate hello_nf-core to nf-core tools 4.0.2 + v2 parser#970

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vdauwera merged 45 commits into
masterfrom
hello-nf-core-tools-4.0
Jul 4, 2026
Merged

Migrate hello_nf-core to nf-core tools 4.0.2 + v2 parser#970
vdauwera merged 45 commits into
masterfrom
hello-nf-core-tools-4.0

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@pinin4fjords

@pinin4fjords pinin4fjords commented Jun 23, 2026 •
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Modernizes the hello_nf-core course from nf-core tools 3.5.2 → 4.0.2 so it runs under the Nextflow 26.04 default v2 parser, removing the NXF_SYNTAX_PARSER=v1 workaround.

What changed

  • Solutions regenerated against the nf-core 4.0.2 template + nf-schema 2.7.2; all 5 (core-hello-start, part2-part5) verified running to completion under the v2 parser on native x86.
  • validate_params: the --validate_params false CLI flag is a no-op under v2 (bare CLI values are typed as strings; "false" is truthy - Using strict syntax causes template to raise an error when setting boolean options on CLI nf-core/tools#4100). Parts 2-4 now set validate_params = false in config (a real boolean), preserving the Part 5 lesson that teaches the schema-validation transformation. The CLI flag is gone from all commands.
  • Docs (Parts 1-5) regenerated from genuine 4.0.2/v2 runs, including the new nf-core/tools version 4.0.2 create banner and the Generated container configs... line.
  • Orientation rewritten: drops the v1 instruction, documents that the course runs under the v2 default, and adds guidance that boolean params must be set via -params-file/config, not bare CLI flags (the v2 string-typing behavior - it also affected Part 1's --skip_trim, now shown via a params file).
  • Devcontainer uv-tools pin → nf-core==4.0.2.

Known 4.0 behavior documented

nf-core modules install raises NotADirectoryError on the course's single-file local modules (4.0 expects directory-style); the install still completes, so Part 3 now verifies via modules.json with a warning admonition.

Not verified (inherent)

Interactive nf-core TUIs (pipelines create, schema build, modules create) can't be driven headlessly; their banners/versions are genuine 4.0.2, the click-through steps are unchanged.

🤖 Generated with Claude Code

pinin4fjords and others added 30 commits June 23, 2026 12:07
@pinin4fjords
Bump NXF_VER to 26.04.4 in devcontainers [skip ci]
ba91a90
@pinin4fjords
docs: reflect v2 parser as default from Nextflow 26.04 in version not…
6d21f0d 
…es [skip ci]
@pinin4fjords
docs(hello_nextflow): refresh tutorial output for Nextflow 26.04 [ski…
673bd79 
…p ci]
@pinin4fjords
docs(hello_nextflow): clarify v2 parser is default from 26.04 in trou…
3db993b 
…bleshooting note [skip ci]
@pinin4fjords
docs(hello_nextflow): correct truncated Outputs blocks with full real…
bb54f7d 
… 26.04 output [skip ci]
@pinin4fjords
docs(nextflow_run): refresh tutorial output for Nextflow 26.04 [skip ci]
d2a8d03
@pinin4fjords
docs(nf4_science): refresh genomics + rnaseq output for Nextflow 26.0…
f56e753 
…4 [skip ci]
@pinin4fjords
docs(hello_nextflow): fix stale 'greeting' param to 'input' in lesson…
cf2aafd 
… 4 snippets [skip ci]
@pinin4fjords
docs: fix cowpy demos to use stdin so documented output is genuine
8bb0262 
The positional form 'cowpy "Hello Containers"' does not put the text in the
speech bubble (cowpy reads the message from stdin); it printed the cowacter
self-description. Use the stdin form, matching how the pipeline module invokes
cowpy, so the documented output is what the command actually produces. [skip ci]
@pinin4fjords
docs(side_quests): refresh nf_test + plugin_development for Nextflow …
14c5d41 
…26.04 [skip ci]
@pinin4fjords
docs(side_quests): refresh working_with_files for Nextflow 26.04 [ski…
8d7437e 
…p ci]
@pinin4fjords
docs(hello_nf-core): refresh tutorial output for Nextflow 26.04 (runs…
d6eacef 
… under v1 parser) [skip ci]
@pinin4fjords
docs(hello_nf-core): clarify v1 parser requirement overrides 26.04 v2…
a489d62 
… default [skip ci]
@pinin4fjords
docs(side_quests): refresh metadata for Nextflow 26.04 [skip ci]
ffd9b23
@pinin4fjords
docs(side_quests): refresh debugging + dev_environment for Nextflow 2…
9b17550 
…6.04 [skip ci]
@pinin4fjords
docs(side_quests): refresh essential_scripting_patterns for Nextflow …
b72b36b 
…26.04 [skip ci]
@pinin4fjords
docs(side_quests): verify workflows_of_workflows on Nextflow 26.04 [s…
e656fb4 
…kip ci]
@pinin4fjords
docs(side_quests): verify+correct splitting_and_grouping for Nextflow…
3a12a21 
… 26.04 [skip ci]
@pinin4fjords
docs(side_quests): add genuine 26.04 hint line to nf_test 2.1 failure…
ff639a1 
… block [skip ci]
@pinin4fjords
Bump NXF_VER to 26.04.4 in local-dev devcontainer [skip ci]
bd9a61a
@pinin4fjords
docs(side_quests): re-verify plugin_development on 26.04; bump broken…
f2db0a2 
… nf-co2footprint 1.2.0->1.3.0 [skip ci]
@pinin4fjords
docs(hello_nf-core): fix Part 1 nextflow-pull layout + genuine demo o…
2ad4d65 
…utput for 26.04 (v1) [skip ci]
@pinin4fjords @claude
ci: run full checks for Nextflow 26.04 bump
3fab718 
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
@pinin4fjords
Merge origin/master into nextflow-26-bump
2a5cc64 
Resolve side-quest conflicts by taking master's content (#960 gremlin fixes,
#961 essential-scripting workflow-output publishing); 26.04 output to be
regenerated from real runs in follow-up commits. [skip ci]
@pinin4fjords
feat(hello_nf-core): migrate solutions to nf-core 4.0.2 template + nf…
daa2cdd 
…-schema 2.7.2, v2-clean

All 5 solutions run to completion under Nextflow 26.04.4 v2 parser. validate_params
handled via config boolean in parts 2-4 (preserves lesson 5's schema-validation exercise);
part 5 keeps the greetings schema + validation on. [skip ci]
@pinin4fjords
docs(side_quests): re-verify nf_test on 26.04 post-merge; fix nf-test…
a90708d 
… hash consistency [skip ci]
@pinin4fjords
docs(side_quests): re-verify debugging on 26.04 post-merge (genuine e…
81e0c34 
…rror text + output) [skip ci]
@pinin4fjords
docs(side_quests): re-verify essential_scripting_patterns on 26.04 po…
b009d41 
…st-merge with #961 publishing [skip ci]
@pinin4fjords
docs(side_quests): fix buggy_workflow error sequence + bad_resources …
b7c54fc 
…prose for v2 static type checking [skip ci]
@pinin4fjords @claude
ci: re-run checks after master merge + side-quest re-verification
001de7f 
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
pinin4fjords and others added 4 commits June 23, 2026 17:44
@pinin4fjords
docs(nf4_science/imaging): bring molkart course to 26.04, v2-clean vi…
988c778 
…a typed params.yaml

Validated end-to-end on native x86 (22-task molkart run). Resolves the v2
integer-param typing issue (--flag value ints arrive as strings under the v2
parser) by switching documented commands to a typed params.yaml; also fixes a
fabricated resume block and a wrong task count. [skip ci]
@pinin4fjords @claude
ci: re-run checks after folding imaging into the bump
5b96226 
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
@pinin4fjords
Merge branch 'nextflow-26-bump' into hello-nf-core-tools-4.0
0eacc7b
@pinin4fjords
feat(hello_nf-core): migrate course docs to nf-core 4.0.2 + v2 parser
9b485e3 
Runs under the 26.04 default v2 parser (no NXF_SYNTAX_PARSER=v1). Boolean params
set via params-file/config instead of bare CLI flags (which the v2 parser types as
strings). Orientation rewritten to v2 + nf-core 4.0.2; devcontainer pin -> 4.0.2.
All console output regenerated from genuine 4.0.2/v2 runs on x86. [skip ci]
Base automatically changed from nextflow-26-bump to master July 3, 2026 11:18
@pinin4fjords pinin4fjords marked this pull request as ready for review July 3, 2026 11:20
@pinin4fjords
Merge remote-tracking branch 'origin/master' into hello-nf-core-tools…
a3ded7e 
…-4.0

# Conflicts:
#	docs/en/docs/hello_nf-core/00_orientation.md
#	docs/en/docs/hello_nf-core/01_run_demo.md
#	docs/en/docs/hello_nf-core/02_rewrite_hello.md
#	docs/en/docs/hello_nf-core/03_use_module.md
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Nextflow linting complete!

⚠️ 34 files had 51 warnings
✅ 189 files had no errors
🔧 136 files would be changed by auto-formatting

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

View all 51 issues
Type Location Message
Warning hello-nf-core/solutions/composable-hello/hello.nf:36:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part2/workflows/hello.nf:44:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part2/workflows/hello.nf:68:17 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part3/workflows/hello.nf:45:55 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part3/workflows/hello.nf:53:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part3/workflows/hello.nf:77:17 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part4/modules/local/cowpy/main.nf:30:9 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part4/workflows/hello.nf:50:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part4/workflows/hello.nf:74:17 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part5/modules/local/cowpy/main.nf:30:9 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-part5/workflows/hello.nf:50:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part5/workflows/hello.nf:74:17 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning hello-nf-core/solutions/core-hello-start/workflows/hello.nf:18:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-start/workflows/hello.nf:45:9 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-start/workflows/hello.nf:54:5 Emit name should be omitted when there is only one emit
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/metadata/2.4/main.nf:42:22 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/metadata/3.2/main.nf:42:22 Parameter was not used -- prefix with _ to suppress warning
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/hello-config.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/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 
@@ -6,7 +6,7 @@ conda.enabled = true
 */
 process {
     memory = 1.GB
-    withName: 'cowpy' {
+    withName: cowpy {
         memory = 2.GB
         cpus = 2
     }
@@ -32,11 +32,7 @@ profiles {
     univ_hpc {
         process.executor = 'slurm'
         conda.enabled = true
-        process.resourceLimits = [
-            memory: 750.GB,
... (truncated)
hello-nf-core/solutions/composable-hello/hello.nf
View 
@@ -14,9 +14,7 @@ include { collectGreetings } from './modules/collectGreetings.nf'
 include { cowpy } from './modules/cowpy.nf'
 
 workflow HELLO {
-
     take:
-    // channel of greetings
     greeting_ch
 
     main:
hello-nf-core/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)
hello-nf-core/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()
hello-nf-core/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}'
     """
 }
hello-nf-core/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}
     """
 }
hello-nf-core/solutions/composable-hello/modules/sayHello.nf
View 
@@ -13,6 +13,6 @@ process sayHello {
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
     """
 }
hello-nf-core/solutions/core-hello-part2/conf/base.config
View 
@@ -11,13 +11,13 @@
 process {
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = { 1      * task.attempt }
-    memory = { 6.GB   * task.attempt }
-    time   = { 4.h    * task.attempt }
+    cpus = { 1 * task.attempt }
+    memory = { 6.GB * task.attempt }
+    time = { 4.h * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104 + (175..177)) ? 'retry' : 'finish' }
-    maxRetries    = 1
-    maxErrors     = '-1'
+    maxRetries = 1
... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/modules.config
View 
@@ -12,10 +12,5 @@
 
 process {
 
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
+    publishDir = [path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }]
 }
hello-nf-core/solutions/core-hello-part2/conf/test.config
View 
@@ -11,21 +11,17 @@
 */
 
 process {
-    resourceLimits = [
-        cpus: 2,
-        memory: '4.GB',
-        time: '1.h'
-    ]
+    resourceLimits = [cpus: 2, memory: '4.GB', time: '1.h']
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name = 'Test profile'
... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/test_full.config
View 
@@ -11,7 +11,7 @@
 */
 
 params {
-    config_profile_name        = 'Full test profile'
+    config_profile_name = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
hello-nf-core/solutions/core-hello-part2/main.nf
View 
@@ -13,9 +13,9 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { HELLO  } from './workflows/hello'
+include { HELLO } from './workflows/hello'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_hello_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_hello_pipeline'
+include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline'
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -26,7 +26,6 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_hell
 // WORKFLOW: Run main analysis pipeline depending on type of input
 //
... (truncated)
hello-nf-core/solutions/core-hello-part2/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()
hello-nf-core/solutions/core-hello-part2/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}'
     """
 }
hello-nf-core/solutions/core-hello-part2/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)
hello-nf-core/solutions/core-hello-part2/modules/local/sayHello.nf
View 
@@ -13,6 +13,6 @@ process sayHello {
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
     """
 }
hello-nf-core/solutions/core-hello-part2/nextflow.config
View 
@@ -11,30 +11,30 @@ params {
 
     // TODO nf-core: Specify your pipeline's command line flags
     // Input options
-    input                      = null
+    input = null
 
     // Boilerplate options
-    outdir                       = null
-    publish_dir_mode             = 'copy'
-    monochrome_logs              = false
-    help                         = false
-    help_full                    = false
-    show_hidden                  = false
-    version                      = false
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf
View 
@@ -8,13 +8,13 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-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'
-include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+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'
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
View 
@@ -10,9 +10,9 @@
 
 workflow UTILS_NEXTFLOW_PIPELINE {
     take:
-    print_version        // boolean: print version
-    dump_parameters      // boolean: dump parameters
-    outdir               //    path: base directory used to publish pipeline results
+    print_version // boolean: print version
+    dump_parameters // boolean: dump parameters
+    outdir //    path: base directory used to publish pipeline results
     check_conda_channels // boolean: check conda channels
 
     main:
@@ -72,10 +72,10 @@ def getWorkflowVersion() {
 //
... (truncated)
hello-nf-core/solutions/core-hello-part2/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)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
View 
@@ -125,12 +125,12 @@ def paramsSummaryMultiqc(summary_params) {
         }
 
     def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
-    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
-    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text     += "plot_type: 'html'\n"
-    yaml_file_text     += "data: |\n"
-    yaml_file_text     += "${summary_section}"
+    yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text += "plot_type: 'html'\n"
+    yaml_file_text += "data: |\n"
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
hello-nf-core/solutions/core-hello-part2/workflows/hello.nf(truncated)
hello-nf-core/solutions/core-hello-part3/conf/base.config(truncated)
hello-nf-core/solutions/core-hello-part3/conf/modules.config(truncated)
hello-nf-core/solutions/core-hello-part3/conf/test.config(truncated)
hello-nf-core/solutions/core-hello-part3/conf/test_full.config(truncated)
hello-nf-core/solutions/core-hello-part3/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/local/collectGreetings.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/local/convertToUpper.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/local/cowpy.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/local/sayHello.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/nf-core/find/concatenate/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf(truncated)
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hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nf...*[Comment body truncated]*

vdauwera and others added 9 commits July 3, 2026 16:57
@vdauwera @claude
review(hello_nf-core): fix path leak, boolean warning placement, Part…
5b72fd2 
… 3 section 1.4, v2 compat note

- Fix leaked author path in Part 3 run output (replace /home/ubuntu/hnc-scratch with codespace paths)
- Move boolean params warning from orientation to Part 1 section 3.1.2 where it first applies
- Restructure Part 3 section 1.4: tip and NotADirectoryError explanation as prose, add modules.json content, rewrite nf-core modules list local note
- Add v2 parser compatibility note for outputDir/workflow.output.mode in Part 2 section 5.4

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
feat(hello_nf-core): provide my_params.yml and malformed_samplesheet.…
6cd13ab 
…csv as course materials

Replace learner-created files with pre-provided equivalents in Part 1:
- Add my_params.yml (skip_trim: true) and malformed_samplesheet.csv to hello-nf-core/
- Update Part 1 section 3.1.2 and 3.1.4 to reference provided files instead of instructing learners to create them
- Update orientation directory tree and file descriptions

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
chore(hello_nf-core): update screenshots and minor wording fix in Part 3
d0800ab 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
feat(hello_nf-core): provide custom.config and combine config overrid…
770e263 
…e exercises in Part 1

- Add custom.config (FASTQC resource override + SEQTK_TRIM ext.args) to hello-nf-core/
- Merge sections 3.2.1 and 3.2.2 into a single exercise showing both overrides at once
- Update orientation directory tree and file descriptions

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
docs(hello_nf-core): clarify Part 1 is a standalone stopping point fo…
e7e6d83 
…r pipeline users

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
fix(hello_nf-core): update Part 1 docs to match nf-core/demo 1.2.0 ou…
39f0d91 
…tputs

- Fix process counts and add COWPY to all run outputs (1.2.0 added COWPY process)
- Remove multiqc_plots from demo-results tree (no longer produced in 1.2.0)
- Update directory count from 13 to 12 accordingly
- Update conf/ listing to include container config files added in 1.2.0
- Update test.config snippet: trailing comma in resourceLimits, aligned input field
- Update modules.config snippet: ext.args spacing to match actual file
- Add missing ' -- Check .nextflow.log' line to validation error outputs
- Fix tree ordering to Linux case-sensitive sort (uppercase before lowercase)
- Fix 'three tools' → 'four tools' and backtick process names in prose
- Fix 'Don't worry' to neutral phrasing
- Update docs link from 1.1.0 to 1.2.0

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera
tiny fixes
6a0ab0b
@vdauwera
tiny tweak
58bc663
@vdauwera
minor tweaks
765cdb8
@vdauwera vdauwera self-requested a review July 4, 2026 03:15
@vdauwera @claude
docs(hello_nf-core): convert note admonitions to info, add v2 parser …
b55c2cd 
…compat warning, fix tree ordering

- Replace all !!! note with !!! info across Parts 2-5 (18 instances)
- Add v2 parser compatibility warning to orientation page
- Fix tree ordering in Part 2 core-hello scaffold (README.md, docs/ subdir)
- Revert style fix to 'Don't worry' line in Part 1

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
vdauwera
vdauwera approved these changes Jul 4, 2026
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Made some additional refinements and added a note of caution about potentially needing to set syntax parser to v1 to run other nf-core pipelines

@vdauwera vdauwera merged commit 1717483 into master Jul 4, 2026
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@vdauwera vdauwera deleted the hello-nf-core-tools-4.0 branch July 4, 2026 03:35
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@pinin4fjords @vdauwera