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Branch to accumulate minor fixes from Summit training - #945

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vdauwera merged 27 commits into
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gvda-bos-summit-fixes-apr26
Jul 6, 2026
Merged

Branch to accumulate minor fixes from Summit training#945
vdauwera merged 27 commits into
masterfrom
gvda-bos-summit-fixes-apr26

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@vdauwera

@vdauwera vdauwera commented Apr 28, 2026

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robsyme and others added 12 commits April 27, 2026 18:51
@robsyme
Fix stale .md cross-references to renamed side quests
4472208 
PR #761 restructured side quests so `<name>.md` became `<name>/index.md`
(URLs now `/side_quests/<name>/`), but missed updating cross-references
that still point at the old `.md` filenames. Those links 404 on the
deployed site — e.g., the "Debugging Nextflow Workflows" link from
working_with_files.

Replaces every stale `<segment>.md` link target with `<segment>/` across
the English docs. Two segment names also rename: `nf-test.md` → `nf_test/`
(the directory uses an underscore, not a hyphen).

Translations are AI-regenerated each release, so they're not touched here.

Affected English pages:
  side_quests/working_with_files/index.md
  side_quests/dev_environment/index.md
  nf4_science/genomics/02_per_sample_variant_calling.md
  hello_nextflow/02_hello_channels.md
  hello_nextflow/06_hello_config.md
  nextflow_run/next_steps.md
  nextflow_run/03_config.md
  hello_nf-core/02_rewrite_hello.md
  hello_nf-core/04_make_module.md

Verified end-to-end against a local mkdocs build: every previously broken
target now returns 200 (debugging, nf_test, metadata, workflows_of_workflows,
working_with_files), and the user's specific link from working_with_files
now resolves to /side_quests/debugging/.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Signed-off-by: Rob Syme <rob.syme@gmail.com>
@vdauwera
Fix links to metadata and wow SQ
6f38472
@vdauwera
Add index.md to the side quest links
8fa379a
@vdauwera
Merge branch 'master' into fix/stale-side-quest-md-links
b7c31e9
@vdauwera
Merge branch 'gvda-fix-links-hnf-rewrite' into fix/stale-side-quest-m…
1f7f351 
…d-links
@vdauwera
Merge branch 'fix/stale-side-quest-md-links' of https://github.com/ne…
f7f9cce 
…xtflow-io/training into fix/stale-side-quest-md-links
@vdauwera
One more link fix
bb59caa
@vdauwera
Make all internal links point to the file
5a24fb0
@vdauwera
Fix remaining broken links
4fdcb02
@vdauwera
last links to fix (I live in hope)
81bc393
@vdauwera
Minor fixes to the training docs
e9f6eec 
Nothing functional, just text, formatting etc
@vdauwera
Merge branch 'master' into gvda-bos-summit-fixes-apr26
628e74b
@vdauwera vdauwera self-assigned this Apr 28, 2026
@vdauwera vdauwera added documentation Improvements or additions to documentation cross-cutting labels Apr 28, 2026
@vdauwera
vdauwera marked this pull request as draft April 28, 2026 02:20
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Nextflow linting complete!

⚠️ 34 files had 47 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 47 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: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: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: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: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)
hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nextflow_pipeline/main.nf(truncated)
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hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/workflows/hello.nf(truncated)
hello-nf-core/solutions/core-hello-part4/conf/base.config(truncated)
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hello-nf-core/solutions/core-hello-part4/modules/local/cowpy.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/local/cowpy/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/local/sayHello.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/nf-core/find/concatenate/main.nf(truncated)
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vdauwera added 12 commits July 5, 2026 22:47
@vdauwera
fix(working_with_files): correct hl_lines and stale comment in side q…
b939f85 
…uest

Section 6.4 Before/After blocks highlighted the closing brace instead of
the changed path{} line; section 5.1 Before block's comment still said
fromFilePairs while the code it labels uses fromPath.
@vdauwera
Merge remote-tracking branch 'origin/master' into gvda-bos-summit-fix…
10cfcba 
…es-apr26
@vdauwera
minor tweaks
226d046
@vdauwera
fix(metadata): correct hl_lines and heading backtick consistency
3abd1b5 
Section 1.5.1 Before block was missing a highlight for the publish:
line change; a few headings referencing COWPY/multiMap lacked
backticks used consistently elsewhere in the doc.
@vdauwera
fix(splitting_and_grouping): correct hl_lines, broken filter snippet,…
14ea3b5 
… and backtick

Section 1.1 After block was missing the highlight for the
ch_samplesheet -> ch_samples rename. The Summary's filter example used
`it.type`, which throws at runtime since channel elements are
[meta, file] tuples, not the meta map itself. Also backtick subMap for
consistency with the rest of the doc.
@vdauwera
fix(metadata): correct explanation of meta map key when CSV column is…
eb43867 
… missing

The map operation hardcodes character: row.character, so the key is
always created; only its value is null when the column is absent from
the datasheet. The prior wording claimed the key itself was never
created, which contradicts the actual code shown just above it.
@vdauwera
fix(splitting_and_grouping): correct sample naming and missing comma …
7c71264 
…in illustrative snippet

Section 3.5's data structure example used sampleC/sampleC_rep1_*.bam,
which doesn't match the patientA/B/C naming used everywhere else in
the lesson and in the actual samplesheet. Also add the comma missing
between the second and third list elements.
@vdauwera
fix: three instructional inconsistencies across side quests
0eb0050 
- working_with_files: section 5.2 explicitly drops readNum as unneeded,
  but section 6 and the Summary silently reintroduced it as unused dead
  code. Remove it consistently from all post-5.2 destructuring.
- splitting_and_grouping: the Summary's join examples used
  tumor_ch.join(normal_ch), the reverse of the order taught and
  explained in the lesson body (normal_ch.join(tumor_ch)). Fix order.
- metadata: correct an overstated claim that adding a datasheet column
  automatically surfaces it in the meta map; the map operation itself
  also needs updating, only the process interface stays unchanged.
@vdauwera
fix(splitting_and_grouping): finish sampleA/B/C -> patientA/B/C cleanup
8ab2966 
Sections 3.2 and 5 still referenced sampleA/B/C in prose and an
illustrative snippet, left over from before the lesson was renamed to
use patientA/B/C throughout. Only the section 3.5 occurrence was
caught in the previous pass.
@vdauwera
fix(working_with_files): consistently use patient as the destructured…
6dcb547 
… variable name

Section 4.3 introduces the tokenized filename variable as `patient`
and explains the choice explicitly in prose, but sections 5.1 onward
(including the Summary's Key patterns code) reverted to `sample`
without explanation, leftover from an earlier draft.
@vdauwera
fix: align channel variable names in summaries with lesson body conve…
1b95aa2 
…ntion

splitting_and_grouping: the Summary used normal_ch/tumor_ch/samples_ch/
intervals_ch (suffix style), contradicting the lesson's own stated
rule to use a ch_ prefix for all channel variables, and the naming
used consistently throughout the lesson body. Renamed to
ch_normal_samples/ch_tumor_samples/ch_joined_samples/ch_intervals.

working_with_files: the Summary introduced ch_pairs for the
fromFilePairs result, but the lesson body consistently calls this
channel ch_files. Renamed to match.
@vdauwera
fix: consistency issues found in nf_test, workflows_of_workflows, dev…
9b5c92d 
…_environment

nf_test: drop a leftover data/ prefix on greetings.csv (no such
subdirectory exists), correct "three processes" to the actual two
(sayHello, convertToUpper), and align "module-level" terminology with
the "process" wording used throughout the body and by nf-test itself.

workflows_of_workflows: fix a leftover "messages" comment that should
say "greetings" (matching every other reference in the same code
block), and correct "four things need to change" to "three", matching
the doc's own later recap and the actual three edit subsections.

dev_environment: normalize three "VSCode" spellings to "VS Code" for
consistency with the ~30 other mentions in the doc.
vdauwera and others added 3 commits July 6, 2026 01:59
@vdauwera
docs(nf_test): add version-requirement note for nf-test compatibility
714a365 
The training container currently bundles nf-test 0.9.2, whose
generated process-test harness uses spread-operator syntax
incompatible with Nextflow 26.04's default strict parser, causing a
misleading Script compilation failed error instead of the documented
test outcome. Flag the actual requirement (0.9.3+) up front so readers
can self-diagnose and upgrade before hitting it.
@vdauwera @claude
fix(hello_nextflow): correct resume example, before-snippet, and outp…
01d716e 
…ut paths

Found by running through all of hello-nextflow in the training container:

- 01_hello_world.md: the -resume example omitted --input, so it wouldn't
  actually produce the documented cache hit given the immediately
  preceding command
- 02_hello_channels.md: "Before" snippet was missing the params{} wrapper
  around the input declaration
- 03_hello_workflow.md: COLLECTED-output.txt file titles were missing the
  hello_workflow/ subdirectory, one had wrong-case content, and a quiz
  anchor pointed to a renamed heading

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@vdauwera @claude
fix(hello_nf-core): correct doc/behavior mismatches found via contain…
33bf0e7 
…er walkthrough

Ran through all six hello-nf-core lessons in the real training container
and fixed confirmed discrepancies between the docs and actual execution:

- 01_run_demo.md: removed a stray unstable text fragment from --help output
  caused by Rich's live-rendering getting corrupted under non-interactive capture
- 02_rewrite_hello.md: fixed hl_lines miscounts and missing backticks
- 03_use_module.md: fixed missing INFO lines in `nf-core modules info` output,
  a broken import-statement ordering/alignment, an unquoted admonition title,
  stale linenums/comment text drifted from the core-hello-part2 checkpoint, and
  converted the "Checking installed modules" admonition to plain prose showing
  the actual command and output (verified: modules list local only shows
  registry-tracked modules, unrelated to the local module's file layout)
- 04_make_module.md: fixed wrong linenums, hl_lines miscounts, and
  capitalization/backtick inconsistencies
- 05_input_validation.md: fixed JSON indentation and a wrong parameter tag
  shown in a success-output example
- solutions/core-hello-part{2,3,4,5}: fixed Channel.topic -> channel.topic,
  a regression from the correctly-generated core-hello-start baseline that
  had propagated through every downstream checkpoint

Also updated the docker-setup skill to read the training image reference
from the current branch's devcontainer.json (like NXF_VER already does)
instead of hardcoding a tag, so container setup always matches what the
branch under test actually pins.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@vdauwera
vdauwera marked this pull request as ready for review July 6, 2026 08:02
@vdauwera

vdauwera commented Jul 6, 2026

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These are all trivial fixes made by claude which i've double-checked and feel confident in.

@vdauwera
vdauwera merged commit c111c5b into master Jul 6, 2026
9 checks passed
@vdauwera
vdauwera deleted the gvda-bos-summit-fixes-apr26 branch July 6, 2026 08:14
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@vdauwera @robsyme