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Fix issues in debugging side quest#771

Merged
pinin4fjords merged 16 commits intomasterfrom
fix/debugging-sidequest-walkthrough-fixes
Jan 13, 2026
Merged

Fix issues in debugging side quest#771
pinin4fjords merged 16 commits intomasterfrom
fix/debugging-sidequest-walkthrough-fixes

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@pinin4fjords
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@pinin4fjords pinin4fjords commented Jan 12, 2026

Summary

Fixes issues found during tutorial walkthrough testing of the debugging side quest.

Changes

  • docs/side_quests/debugging.md: Fix admonition syntax - remove trailing colon from !!! note:
  • side-quests/solutions/debugging/buggy_workflow.nf: Reduce loop iterations from 1,000,000 to 10,000 so the solution completes within the 100s time limit

Issues Fixed

Issue Severity Fix Applied
Invalid admonition syntax !!! note: Minor Removed trailing colon
Solution times out (heavyProcess exceeds 100s) Warning Reduced iterations to 10,000

Testing

  • Tutorial walkthrough completed successfully after fixes
  • All example scripts execute as documented
  • Solution file runs to completion (15/15 processes)
  • Output matches documentation

🤖 Generated with Claude Code

pinin4fjords and others added 14 commits January 12, 2026 10:20
@pinin4fjords @claude
Add run-tutorial Claude skill for walkthrough testing
c7b9b04 
New skill that simulates a learner's experience by:
- Progressively building code section by section
- Running commands exactly as documented
- Verifying "Before" state matches before applying changes
- Comparing final results against solution files
- Cleaning up working directories after successful runs

Uses Docker container with dynamically-determined NXF_VER
from devcontainer.json to match the learner environment.
References existing skills for specialized checks.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Make run-tutorial skill invoke validation and test skills
50ebbc7 
Instead of just recommending follow-up skills, the walkthrough now:
- Invokes /validate in Phase 1 to check highlights, structure, pedagogy
- Invokes /test-example in Phase 3 on solution files
- Reports results from both skills in the output summary

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix run-tutorial skill: add UTF-8 locale and improve reporting
063c89c 
Discovered during workflow_outputs tutorial walkthrough:

- Add UTF-8 locale settings (LANG=C.UTF-8, LC_ALL=C.UTF-8) to Docker
  commands to handle non-ASCII characters like "Holà" - without these,
  Nextflow fails with "Malformed input or unmappable characters" error
- Clean up existing container before starting to avoid conflicts
- Improve output format to report actual results from /validate skill
  (heading count, hl_lines blocks checked, TODO counts, etc.)
- Improve output format to report actual results from /test-example skill
  (process counts, resume verification, output checks)
- Organize issues by severity (Critical/Warning/Minor)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Exclude .claude skill files from heading check
ca06387 
Skill files are internal instructions for Claude, not student-facing
training materials. They don't need to follow the same heading
numbering conventions as lesson content.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add Phase 4: Propose fixes and create PR
94993fb 
When issues are found during tutorial walkthrough:
- Categorize issues as auto-fixable vs requiring manual review
- Present proposed fixes to user in a clear table format
- Ask user for approval before making any changes
- Allow user to review/modify fixes one at a time
- Create PR only after user approval

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords
prettier
06d9221
@pinin4fjords
Update SKILL.md for linting
17aee07
@pinin4fjords @claude
Add Docker-outside-of-Docker (DooD) documentation for local testing
4cf120e 
- Document DooD setup for tutorials with containerized processes
- Explain path matching requirement for sibling containers
- Add Apple Silicon platform emulation instructions
- Include troubleshooting table for common DooD errors

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Strengthen incremental testing requirements in run-tutorial skill
f07e84e 
- Add CRITICAL note at start of Phase 2 about completing all steps per section
- Add new step 2.6 "Confirm Section Complete Before Proceeding"
- Expand Notes section with explicit "ONE SECTION AT A TIME" and "Test after EVERY change"
- Add guidance to test even when tutorial doesn't explicitly say to run

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords
Prettier
16c865f
@pinin4fjords
Update SKILL.md with spaces
f1ad2de
@pinin4fjords
Merge branch 'master' into add-run-tutorial-skill
a13b4a5
@pinin4fjords @claude
Link validate skill to check-highlights skill
8dc082a 
- Add task 6 to validate skill to invoke /check-highlights for comprehensive hl_lines validation
- Simplify run-tutorial skill to consolidate validate references since validate now handles highlights

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix issues in debugging side quest
b4bba6a 
- Fix admonition syntax: remove trailing colon from `!!! note:`
- Reduce heavyProcess loop iterations from 1,000,000 to 10,000 so solution
  completes within the 100s time limit

Found during tutorial walkthrough testing.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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github-actions bot commented Jan 12, 2026 •
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Nextflow linting complete!

❌ 4 files had 21 errors
✅ 165 files had no errors
🔧 149 files would be changed by auto-formatting

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

View all 21 issues
Type Location Message
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:11:1 Invalid include source: '/home/runner/work/training/training/hello-nextflow/solutions/5-hello-containers/modules/sayHello.nf'
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:12:1 Invalid include source: '/home/runner/work/training/training/hello-nextflow/solutions/5-hello-containers/modules/convertToUpper.nf'
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:13:1 Invalid include source: '/home/runner/work/training/training/hello-nextflow/solutions/5-hello-containers/modules/collectGreetings.nf'
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:24:5 sayHello is not defined
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:27:5 convertToUpper is not defined
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:27:20 sayHello is not defined
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:30:5 collectGreetings is not defined
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:30:22 convertToUpper is not defined
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:33:5 collectGreetings is not defined
Error hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf:36:11 collectGreetings is not defined
Error hello-nf-core/solutions/core-hello-part2/nextflow.config:154:17 Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/core-hello-part2/conf/test_full.config'
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:1:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/validate_name.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:2:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/say_hello.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:3:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/timestamp_greeting.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:11:24 VALIDATE_NAME is not defined
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:12:24 SAY_HELLO is not defined
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:13:26 TIMESTAMP_GREETING is not defined
Error side-quests/solutions/workflows_of_workflows/workflows/transform.nf:1:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/say_hello_upper.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/transform.nf:2:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/reverse_text.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/transform.nf:10:20 SAY_HELLO_UPPER is not defined
Error side-quests/solutions/workflows_of_workflows/workflows/transform.nf:11:23 REVERSE_TEXT is not defined
View formatting changes
FileDiff
hello-nextflow/solutions/1-hello-world/hello-world-3.nf
View 
@@ -8,7 +8,7 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     output:
-        path 'output.txt'
+    path 'output.txt'
 
     script:
     """
hello-nextflow/solutions/1-hello-world/hello-world-4.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path 'output.txt'
+    path 'output.txt'
 
     script:
     """
-    echo '$greeting' > output.txt
+    echo '${greeting}' > output.txt
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path 'output.txt'
+    path 'output.txt'
 
     script:
     """
-    echo '$greeting' > output.txt
+    echo '${greeting}' > output.txt
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf
View 
@@ -8,14 +8,14 @@ process convertToUpper {
     publishDir 'results', mode: 'copy'
 
     input:
-        path input_file
+    path input_file
 
     output:
-        path "UPPER-${input_file}"
+    path "UPPER-${input_file}"
 
     script:
     """
-    cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
+    cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf
View 
@@ -8,15 +8,15 @@ process collectGreetings {
     publishDir 'results', mode: 'copy'
 
     input:
-        path input_files
-        val batch_name
+    path input_files
+    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
 
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf
View 
@@ -15,8 +15,8 @@ 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] }
 
     // emit a greeting
     sayHello(greeting_ch)
@@ -28,5 +28,5 @@ workflow {
     collectGreetings(convertToUpper.out.collect(), params.batch)
 
     // emit a message about the size of the batch
... (truncated)
hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf
View 
@@ -6,15 +6,15 @@ process collectGreetings {
     publishDir 'results', mode: 'copy'
 
     input:
-        path input_files
-        val batch_name
+    path input_files
+    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
 
... (truncated)
hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf
View 
@@ -8,13 +8,13 @@ process convertToUpper {
     publishDir 'results', mode: 'copy'
 
     input:
-        path input_file
+    path input_file
 
     output:
-        path "UPPER-${input_file}"
+    path "UPPER-${input_file}"
 
     script:
     """
-    cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
+    cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
... (truncated)
hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf
View 
@@ -8,13 +8,13 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/5-hello-containers/modules/cowpy.nf
View 
@@ -8,14 +8,14 @@ process cowpy {
     container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273'
 
     input:
-        path input_file
-        val character
+    path input_file
+    val character
 
     output:
-        path "cowpy-${input_file}"
+    path "cowpy-${input_file}"
 
     script:
     """
... (truncated)
hello-nextflow/solutions/6-hello-config/modules/cowpy.nf
View 
@@ -9,14 +9,14 @@ 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/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 
@@ -15,6 +15,6 @@ 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 
@@ -17,6 +17,6 @@ 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 
@@ -15,6 +15,6 @@ 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) ? 'retry' : 'finish' }
-    maxRetries    = 1
-    maxErrors     = '-1'
+    maxRetries = 1
... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/modules.config
View 
@@ -15,7 +15,6 @@ 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 }
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
     ]
-
 }
hello-nf-core/solutions/core-hello-part2/conf/test.config
View 
@@ -14,18 +14,18 @@ process {
     resourceLimits = [
         cpus: 2,
         memory: '4.GB',
-        time: '1.h'
+        time: '1.h',
     ]
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
... (truncated)
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 
@@ -15,6 +15,6 @@ 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 
@@ -17,6 +17,6 @@ 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/core-hello-part2/modules/local/sayHello.nf
View 
@@ -15,6 +15,6 @@ process sayHello {
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
     """
 }
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
View 
@@ -1,9 +1,9 @@
 manifest {
-    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'
+    name = 'nextflow_workflow'
+    author = """nf-core"""
+    homePage = 'https://127.0.0.1'
+    description = """Dummy pipeline"""
+    nextflowVersion = '!>=23.04.0'
+    version = '9.9.9'
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf
View 
@@ -2,30 +2,25 @@
 // Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
 //
 
-include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { paramsSummaryLog } from 'plugin/nf-schema'
 include { validateParameters } from 'plugin/nf-schema'
-include { paramsHelp         } from 'plugin/nf-schema'
+include { paramsHelp } from 'plugin/nf-schema'
 
 workflow UTILS_NFSCHEMA_PLUGIN {
-
     take:
-    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
-    validate_params     // boolean:  validate the parameters
... (truncated)
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side-...*[Comment body truncated]*

vdauwera
vdauwera approved these changes Jan 13, 2026
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good catches!

Haven't run the claude stuff myself but it all looks reasonable

@pinin4fjords pinin4fjords merged commit 0399cf9 into master Jan 13, 2026
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@pinin4fjords pinin4fjords deleted the fix/debugging-sidequest-walkthrough-fixes branch January 13, 2026 18:16
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@vdauwera vdauwera vdauwera approved these changes

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@pinin4fjords @vdauwera