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Draft: Advanced side quests for custom training #756

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@pinin4fjords pinin4fjords commented Jan 7, 2026

⚠️ Draft Material - Not a Merge Candidate

This PR contains custom training content for specific teaching sessions. It is not intended to be merged into the main training materials at this time.

Summary

Three new side quests covering advanced Nextflow topics:

1. Workflow Output Definitions (45 mins)

  • New publish: and output {} block syntax (replacing publishDir)
  • Dynamic paths based on metadata
  • Automatic index file generation (CSV/JSON manifests)

2. Running on Cloud Executors (30 mins)

  • Executor concepts and available options
  • AWS Batch configuration patterns
  • S3 integration, profiles, cost management
  • Conceptual only - no cloud account required

3. Plugin Development (90 mins)

  • Full hands-on plugin creation from scratch
  • Custom functions with @Function annotation
  • Build, test, and local installation
  • Complete working nf-greeting plugin solution included

Additional Changes

  • Added Gradle 8.11 to devcontainer for plugin development support
  • All examples use greetings pipeline (consistent with Hello Nextflow)

Testing

  • ✅ All Nextflow scripts tested and working
  • ✅ Plugin builds and runs successfully
  • ✅ Validation checks pass (heading numbering, formatting)

Notes

Keep on branch for custom training sessions. May be adapted for general availability later.

🤖 Generated with Claude Code

@pinin4fjords @claude
Add advanced side quests for custom training
c160ee8 
Three new side quests for advanced Nextflow topics:

1. Workflow Output Definitions (45 mins)
   - New publish/output block syntax
   - Dynamic paths based on metadata
   - Index file generation

2. Running on Cloud Executors (30 mins)
   - Executor concepts and options
   - AWS Batch configuration patterns
   - S3 integration and cost management
   - Conceptual/config-focused (no cloud account needed)

3. Plugin Development (90 mins)
   - Full hands-on plugin creation
   - Custom functions with @function annotation
   - Build, test, and use locally
   - Complete working nf-greeting plugin solution

Also adds Gradle to devcontainer for plugin development support.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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github-actions bot commented Jan 7, 2026 •
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Nextflow linting complete!

❌ 5 files had 22 errors
✅ 170 files had no errors
🔧 152 files would be changed by auto-formatting

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

View all 22 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/workflow_outputs/main.nf:4:1 Unrecognized feature flag 'nextflow.preview.output'
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)
hello-nf-core/solutions/core-hello-part2/workflows/hello.nf(truncated)
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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/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/cat/cat/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config(truncated)
hello-nf-core/solutions/core-hello-part3/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config(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-part4/modules/nf-core/cat/cat/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config(truncated)
hello-nf-core/solutions/core-hello-part4/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config(truncated)
hello-nf-core/solutions/core-hello-part4/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nextflow_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfcore_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
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hello-nf-core/solutions/core-hello-part5/modules/local/cowpy/main.nf(truncated)
hello-nf-core/solutions/core-hello-part5/modules/local/sayHello.nf(truncated)
hello-nf-core/solutions/core-hello-part5/modules/nf-core/cat/cat/main.nf(truncated)
hello-nf-core/solutions/core-hello-part5/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config(truncated)
hello-nf-core/solutions/core-hello-part5/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config(truncated)
hello-nf-core/solutions/core-hello-part5/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part5/subworkflows/local/utils_nfcore_hello_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nextflow_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nfcore_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
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side-quests/solutions/nf-core/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
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side-quests/solutions/workflow_outputs/modules/greetings.nf(truncated)
side-quests/so...*[Comment body truncated]*

pinin4fjords and others added 27 commits January 7, 2026 12:19
@pinin4fjords @claude
Fix prettier formatting issues
602576d 
- Align markdown table columns
- Expand devcontainer JSON to multi-line format

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add Makefile exception to editorconfig
e2801f0 
Makefiles require tabs for recipe indentation (Make syntax requirement).

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add section on using existing plugins to plugin development side quest
3a7921e 
- Add new Section 1 covering plugin usage before development content
- Include examples of installing plugins via plugins {} block
- Show how to import and use plugin functions with include syntax
- Reference nf-schema as practical example (from Hello nf-core)
- Add table of popular community plugins
- Update learning goals to include plugin usage
- Renumber subsequent sections (1→2, 2→3, etc.)

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Remove gradle-sdkman feature from devcontainer config
63fc436 
The gradle-sdkman feature fails with SDKMAN permission errors during build.
Plugin projects include a Gradle wrapper (./gradlew) that downloads Gradle
automatically, so we only need Java pre-installed (provided by java:1 feature).

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add beginner-friendly explanations to plugin development side quest
af6e1fe 
- Add prominent warning that this is an advanced topic
- Add info box explaining Java, Groovy, and Gradle for newcomers
- Highlight that "Using existing plugins" section is most important
- Add detailed breakdown of Groovy syntax with comparisons to Python
- Explain what unit tests are and why they matter
- Add troubleshooting tips for build failures
- Mark "Going further" section as reference material
- Add note that Gradle wrapper downloads Gradle automatically

These changes make the tutorial more accessible to participants
without a software engineering background.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix nextflow plugin create command syntax
8f8f02e 
The command requires both plugin name and organization name arguments.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Update plugin docs to match actual generated structure
876684b 
- Update tree output to show actual generated files
- Change package from nextflow.greeting to training.plugin
- Rename classes to NfGreetingExtension, NfGreetingPlugin, etc.
- Update all code examples and file paths to match
- Update test class names in examples and expected output
- Fix build.gradle example to show correct extensionPoints

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Update build.gradle example to match actual generated output
7df5ffc 
- Use correct plugin version (0.0.1-alpha4)
- Use correct nextflowVersion (24.10.0)
- Remove NfGreetingObserver from extensionPoints (not included by default)
- Add publishing block with registry configuration

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add Before/After comparison for NfGreetingExtension edits
8e261a8 
Show the actual generated template code and the changes needed,
making it clearer what participants need to modify.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix Makefile target: use 'assemble' instead of 'build'
9637bd0 
The generated Makefile uses 'assemble' not 'build' for compilation.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Update build output example with realistic Gradle output
92aa4f4 
Shows the Gradle download on first run and sets expectations
for subsequent faster builds.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add explanations for Gradle build output
450d2f6 
Reassure beginners that deprecation warnings are safe to ignore
and explain what each part of the output means.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix test file section to match actual project structure
c83b467 
- Clarify that we're creating a new test file (not editing existing)
- Use Spock framework syntax to match generated project style
- Add note explaining Spock's given/expect syntax
- Update test output to show Spock-style test names

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Explain Gradle's minimal test output and how to see details
354ef2d 
Gradle hides test details on success, which can confuse beginners.
Added explanation that BUILD SUCCESSFUL means tests passed, with
optional --info flag for verbose output.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Remove misleading --info suggestion, point to HTML report instead
c8e1f75 
The --info flag produces verbose Gradle output, not clean test results.
Instead, point users to the HTML test report for detailed results.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add section on viewing test report with screenshot
a8e66cf 
Show how to use python http.server to view the Gradle test report
in VS Code, with screenshot showing all tests passing.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix: nextflow.config is already configured, not edited
02c32ec 
The starter files already have the plugin configuration.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add Before/After comparison for main.nf edits
e59ac9a 
Shows the starter file and the changes needed to use plugin functions,
with highlighted lines and explanation of key changes.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix nextflow.config section - show Before/After for uncommenting
e36a284 
The starter config has the plugin commented out. Users need to
uncomment it AND add the @0.1.0 version for local plugins.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Update pipeline output with real example
0c92029 
Added note explaining the startup/complete messages come from
the NfGreetingObserver included in the plugin template.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Update output file example with proper formatting
ac5d112 
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add hands-on exercise to 'Using existing plugins' section
e5c1007 
Added section 1.6 with a practical exercise using nf-hello plugin.
Users create a simple workflow that uses the sayHello function,
seeing plugin download and usage in action.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Rewrite plugin exercise as Before/After with use case explanation
7f6005a 
- Added 'Why use plugins instead of local functions?' section
- Restructured exercise to show local function first, then plugin
- Before/After tabs show the code change clearly
- Explains the value proposition: versioned, shareable code

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add explicit touch command to create test file
b9da74a 
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Make 'Going further' section more hands-on with Before/After
0b8d500 
- Connect trace observers to the messages users already saw
- Add Before/After exercise to customize observer messages
- Add table of available observer hooks
- Mark operators as reference (more complex)
- Update publishing section with clearer steps

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Expand 'Going further' section with hands-on exercises for all extens…
1cc04fc 
…ion types

- Add progress table showing coverage of extension types from table 2.1
- Add TaskCounterObserver creation exercise (new file, not editing existing)
- Add custom operator (shoutAll) with full Before/After convention
- Add configurable decorator exercise with Before/After
- Add conceptual coverage of Factories, Executors, and Filesystems
- Update publishing section with complete instructions
- Clean up solution main.nf formatting

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Restructure plugin development doc into clearer sections
0dd514e 
- Fix duplicate 5.4 numbering (install locally → 5.5)
- Split monolithic section 7 into focused sections:
  - Section 7: Trace observers
  - Section 8: Custom operators and factories
  - Section 9: Configuration
  - Section 10: Publishing your plugin
- Add Takeaway/What's next transitions between new sections

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
pinin4fjords and others added 27 commits January 12, 2026 10:17
@pinin4fjords @claude
Clean up plugin development solution files to match tutorial
864b13c 
Remove extra features from solution files that aren't covered in the
tutorial:
- Remove unused prefix/suffix config options from nextflow.config
- Simplify output message in main.nf to match tutorial
- Remove extra comment block from random_id_example.nf

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix and modernize genomics tutorial documentation
f86224c 
## Code block fixes
- Fix 6 incorrect hl_lines values in 02_joint_calling.md
- Fix wrong title in 03_modules.md (tests/main.nf.test → genomics-3.nf)
- Fix wrong language in 04_testing.md (console → groovy)

## Syntax modernization
- Convert 25 Before/After blocks to Material for MkDocs tabbed syntax
  (=== "After" / === "Before") across all 4 parts

Found during tutorial walkthrough validation.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords
Merge branch 'master' into custom-training-advanced-topics
aae9d5d
@pinin4fjords @claude
Add Amazon EKS coverage to cloud executors side quest
c842a21 
- Add sections on EKS fundamentals and configuration (sections 4-5)
- Document PVC-based approach with Amazon EFS for shared storage
- Include Kubernetes RBAC configuration example
- Add eks.config example configuration file
- Update profiles to include EKS option
- Add documentation source links for verification
- Mention Fusion as optional Platform enhancement (not core requirement)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Replace ASCII diagrams with Mermaid in cloud executors
2261d6d 
Convert AWS Batch and EKS architecture diagrams from ASCII art
to Mermaid flowcharts for better maintainability and rendering.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Improve EKS documentation accessibility and focus
aeece25 
- Add warning that EKS is more complex than AWS Batch
- Explain Kubernetes concepts (pods, namespaces, PVCs) for newcomers
- Clarify when to choose EKS vs AWS Batch
- Focus on Nextflow config, not infrastructure setup
- Simplify: "ask your admin for namespace, service account, storage"
- Remove detailed YAML examples (link to docs instead)
- Update summary checklist to match simplified approach

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add AWS authentication section to cloud executors
734997b 
Explain how Nextflow authenticates with AWS:
- Environment variables
- AWS credentials file (~/.aws/credentials)
- IAM instance profile

Clarify distinction between credentials for Nextflow (to submit jobs)
vs jobRole for jobs themselves (to access S3).

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Clarify fallback container purpose in executor configs
f07ac6a 
- Add inline comment explaining container is a fallback
- Explain in docs that most pipelines define per-process containers
- Fallback is useful for simple bash processes without explicit containers

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Clarify that Fusion requires Seqera Platform subscription
76c3ea9 
- Add links to Platform pricing/info
- Update section 7.4 title to indicate Platform feature
- Simplify Fusion code example
- Update takeaway to mention Platform requirement

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Remove section 8 (Practical considerations)
51ec8d0 
Content was generic and not particularly useful for this guide.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix AWS Batch executor configuration syntax
0bd3ffc 
Changed from incorrect executor block syntax to correct process scope:
- executor.name -> process.executor
- executor.queueName -> process.queue
- Consolidated container setting in process block

These corrections align with the official Nextflow documentation.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Address Adam's review comments on plugin development side quest
2a57b00 
- Remove make comparison for Gradle (advanced concept)
- Replace reverseString() with samplesheetToList() as example (more recognizable)
- Reduce hyperbole throughout, get to the point faster
- Add Slack as example for extending pipelines
- Clarify that community can add features without modifying Nextflow core
- Simplify tip about using plugins section
- Add notes about latest version default and runtime download
- Restructure "Try it" section: remove local function comparison,
  use config-only approach, remove CLI flag diversion
- Add note about development burden being on plugin developer
  and Nextflow handling plugin management

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords
Merge branch 'master' into plugin-development-side-quest
4b2b637
@pinin4fjords @claude
Remove 'Popular community plugins' section per Adam's feedback
f34c4c4 
The plugin registry already lists available plugins, so this section
was redundant.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Clean up hyphen phrases and tone down language
d975952 
- Replace em-dash elaborations with periods or semicolons
- Use colons instead of hyphens for list item explanations
- Remove unnecessary trailing explanations
- Simplify sentences to be more direct

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix heading numbering and format tables
a196d96 
- Fix section 2.7 -> 2.6 after removing Popular plugins section
- Run prettier to fix table formatting

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords
Remove plugin development content (will merge from #761)
da4bbee 
Removing plugin files so they can be cleanly merged from the
plugin-development-side-quest branch, which has the reviewed
and updated version.
@pinin4fjords
Merge plugin development from #761
65f88b8
@pinin4fjords
Fix prettier formatting in cloud_executors tables
940682d
@pinin4fjords
Merge branch 'master' into custom-training-advanced-topics
59c26ec
@pinin4fjords @claude
Improve workflow outputs side quest writing style and clarity
062a1fa 
- Remove LLM-style "Let's" phrases throughout
- Add note explaining -output-dir is a native Nextflow feature (vs nf-core's params.outdir convention)
- Add hl_lines to code blocks in section 1.1 highlighting publishDir and meta map pattern

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Use dynamic publishDir closures in workflow outputs starter
8ed5add 
Update the starter code to use publishDir closures with meta.language
for a fairer comparison with workflow output blocks. Both approaches
now demonstrate dynamic paths, so the lesson focuses on the real
benefits of workflow outputs (centralization, index files) rather
than implying publishDir can't do dynamic paths.

- Starter modules/greetings.nf now uses publishDir closures
- Section 1.1 shows dynamic publishDir from the start
- Section 1.2 shows language-organized output
- Section 2 introduces workflow outputs with static paths
- Section 3 restores dynamic organization in the output block

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Use tree instead of find for results directory output
b98e5d7 
Tree provides a clearer visual representation of the directory structure.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Clarify workflow outputs as recommended approach
e9be4c7 
- Remove "dynamic paths" from key benefits (publishDir can do this too)
- Replace comparison table with note that publishDir is legacy
- Recommend workflow outputs for all new pipeline development

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add tip about type-safe configuration with annotations
376d9c2 
Links to official docs for defining custom config as a proper class
with annotations for IDE and linter support.

Addresses review feedback from @adamrtalbot.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Make publishDir legacy status more prominent
60f836f 
Add warning admonition in section 1.3 (Limitations) where readers
decide whether to learn this. Remove redundant note from summary.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Establish workflow outputs as standard in intro sentence
3caaad8 
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords pinin4fjords force-pushed the custom-training-advanced-topics branch from 05053e4 to 3caaad8 Compare January 14, 2026 14:42
pinin4fjords and others added 2 commits January 14, 2026 14:47
@pinin4fjords @claude
Connect metadata explanation to output routing in section 1.1
5ae4867 
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix invalid executor config syntax in cloud executors examples
54a7cab 
- aws.config: Replace invalid executor.queueName with process.queue
- aws.config: Use process.executor instead of executor.name
- local.config: Separate executor selection from resource limits

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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@pinin4fjords