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Split debugging side quest into mini-course; add -dump-hashes lesson#958

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Split debugging side quest into mini-course; add -dump-hashes lesson#958
pinin4fjords wants to merge 2 commits into
masterfrom
debugging-mini-course-and-dump-hashes

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@pinin4fjords

@pinin4fjords pinin4fjords commented May 15, 2026

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Summary

Restructures the Troubleshooting Workflows side quest as a two-lesson mini-course (matching the plugin_development pattern), and adds new coverage of cache-invalidation debugging with -dump-hashes.

The previous single-page side quest was 2659 lines and a slog to read end-to-end. Splitting it into a catalog (Part 1) and a toolkit walkthrough (Part 2) lets readers stop at a sensible boundary, and gives the new -dump-hashes content a natural home alongside the other CLI debugging flags.

Changes

  • index.md is now a short landing page: overview, prerequisites, lesson plan, learning objectives split by lesson, link to Part 1.
  • 01_common_errors.md carries the existing catalog of syntax, channel and process errors (formerly sections 1-3 of the original).
  • 02_debugging_toolkit.md is rewritten end-to-end around a single spine pipeline (sample_processing.nf). Each tool is applied in sequence:
    • Work-directory forensics (formerly §3.4, generic so moved to the toolkit half)
    • -preview for parse-before-run validation
    • debug true for live process output
    • -stub-run for fast iteration without containers
    • -dump-hashes for cache invalidation — new, with three experiments (script comment, resource directive, channel map change) showing exactly which hash component changes and why
    • Systematic four-phase method
    • Practical exercise on buggy_workflow.nf (carried over from before)
  • New example file side-quests/debugging/sample_processing.nf — the spine pipeline used throughout Part 2. Ships intentionally broken (output filename mismatch), so Part 2 opens with a real forensic walkthrough.
  • mkdocs.yml nav: debugging/index.md becomes a nested "Troubleshooting Workflows" section, like plugin_development.

Why the spine pipeline

Each toolkit section in the previous version used a different example file (missing_output.nf, bad_syntax.nf, bad_channel_shape_viewed_debug.nf, missing_software_with_stub.nf). Threading one pipeline through Part 2 lets the lesson feel like a single development journey: you debug it, validate it, instrument it, iterate on it, and then investigate its caching. The cumulative pedagogical effect matches the style of working_with_files, metadata and splitting_and_grouping.

Test plan

  • Heading numbering check passes on all three lessons (uv run .github/check_headings.py)
  • Prettier check passes (npx prettier@3.2.5 --check)
  • Spine pipeline fails as designed with nextflow run sample_processing.nf -profile docker (verified)
  • Pipeline runs end-to-end after the §1 fix (verified)
  • -preview on broken pipeline reports compilation error (verified)
  • debug true + echo streams to terminal (verified)
  • -stub-run succeeds without -profile docker (verified)
  • -dump-hashes Experiment 1 (comment in script) busts cache and changes script hash (verified)
  • -dump-hashes Experiment 2 (memory directive) does not bust cache (verified)
  • -dump-hashes Experiment 3 (upstream .map change) cascades to all downstream tasks (verified)
  • Render locally with MkDocs and review

🤖 Generated with Claude Code

@pinin4fjords @claude
Split debugging side quest into mini-course; add -dump-hashes lesson
2929bb2 
Restructure the Troubleshooting Workflows side quest as a two-lesson
mini-course (matching the plugin_development pattern), and add new
coverage of cache-invalidation debugging using -dump-hashes.

- index.md becomes a short landing page (overview, prerequisites, lesson
  plan, learning objectives split by lesson)
- 01_common_errors.md is the existing catalog of syntax, channel and
  process errors (was sections 1-3 of the original)
- 02_debugging_toolkit.md is rewritten around a single spine pipeline
  (sample_processing.nf) so each tool is applied in sequence: work-dir
  forensics, -preview, debug true, -stub-run, -dump-hashes, systematic
  method, and a practical exercise on buggy_workflow.nf
- new -dump-hashes section walks three experiments (script comment,
  resource directive, channel map change) and shows in each case which
  hash component changes and why

The old single-page index.md was 2659 lines; splitting and re-anchoring
around one spine pipeline makes the second half navigable rather than a
slog.

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

⚠️ 24 files had 53 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 53 issues
Type Location Message
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/local/utils_nfcore_hello_pipeline/main.nf:98:5 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:102:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part2/workflows/hello.nf:43:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part2/workflows/hello.nf:67:17 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/local/utils_nfcore_hello_pipeline/main.nf:98:5 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:102:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part3/workflows/hello.nf:44:55 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part3/workflows/hello.nf:52:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part3/workflows/hello.nf:76:17 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/local/utils_nfcore_hello_pipeline/main.nf:98:5 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:102:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part4/workflows/hello.nf:49:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part4/workflows/hello.nf:73:17 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/local/utils_nfcore_hello_pipeline/main.nf:97:5 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:101:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part5/workflows/hello.nf:49:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part5/workflows/hello.nf:73:17 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:29:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:32:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:68:5 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:102:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:106:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
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:26:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-start/workflows/hello.nf:50:17 Variable was declared but not used
Warning side-quests/solutions/debugging/buggy_workflow.nf:91:44 Implicit closure parameter is deprecated, declare an explicit parameter instead
Warning side-quests/solutions/essential_scripting_patterns/main.nf:59:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/essential_scripting_patterns/main.nf:63:53 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/essential_scripting_patterns/main.nf:68:5 Variable was declared but not used
Warning side-quests/solutions/essential_scripting_patterns/main.nf:69:5 Variable was declared but not used
Warning side-quests/solutions/metadata/1.2/main.nf:5:5 Variable was declared but not used
Warning side-quests/solutions/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 <...*[Comment body truncated]*
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) ? '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)
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hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
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hello-nf-core/solutions/core-hello-part3/modules/local/cowpy.nf(truncated)
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@pinin4fjords @claude
Walkthrough fixes; add summary.md + next_steps.md
044db7a 
Found during /run-tutorial walkthrough of the new mini-course:

Documentation fixes:
- hl_lines corrections in lesson 2 (§1.3, §3.1, §2.2, §5.4): some were
  off by 1-5 lines, highlighting blank lines or closing quotes instead of
  the meaningful content. Recounted from line 1 of each snippet.
- §2.2 syntax error block: updated from v1 parser format to v2 format
  matching what training environments actually produce
  (NXF_SYNTAX_PARSER=v2 / strict syntax parser default)
- §2.2 "Broken" block: added placeholder comment so it matches "Working"
  line count, letting both highlight the same conceptual position
- Process names (COUNT_LINES, REPORT) and directives (memory, cpus)
  backticked in prose (was bare in several places)
- Two bare ??? "Command output" admonitions in §5 changed to
  ??? success "Command output" for consistency

Mini-course structure (matching plugin_development pattern):
- Added summary.md - course-wide recap with error/tool cheat sheets
  and three "easy to forget" reminders
- Added next_steps.md - what to do next, resources, links to other
  training
- Lesson 2 tail trimmed to a "continue to summary" button rather than
  repeating the recap inline
- mkdocs.yml nav updated to include summary.md and next_steps.md

Verified end-to-end via Docker (DooD):
- L2 §1: missing-output failure + work-dir inspection + fix + success
- L2 §2: -preview on working pipeline + preview catching missing brace
- L2 §3: debug true + echo streams to terminal
- L2 §4: -stub-run runs without docker
- L2 §5: baseline -dump-hashes, comment busts cache, memory directive
  preserves cache, upstream .map change cascades downstream
- L2 §7: buggy_workflow.nf produces the documented initial error
- L1 spot-checks: bad_syntax, invalid_process, no_such_var, bad_resources,
  bad_channel_shape all produce their documented errors

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