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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
🔧 153 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)
hello-nf-core/solutions/core-hello-part3/conf/base.config(truncated)
hello-nf-core/solutions/core-hello-part3/conf/modules.config(truncated)
hello-nf-core/solutions/core-hello-part3/conf/test.config(truncated)
hello-nf-core/solutions/core-hello-part3/conf/test_full.config(truncated)
hello-nf-core/solutions/core-hello-part3/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/local/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)
hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfcore_pipeline/main.nf(truncated)
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hello-nf-core/solutions/core-hello-part4/modules/local/cowpy/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/local/sayHello.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/nf-core/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)
hello-nf-core/solutions/core-hello-part4/workflows/hello.nf(truncated)
hello-nf-core/solutions/core-hello-part5/conf/base.config(truncated)
hello-nf-core/solutions/core-hello-part5/conf/modules.config(truncated)
hello-nf-core/solutions/core-hello-part5/conf/test.config(truncated)
hello-nf-core/solutions/core-hello-part5/conf/test_full.config(truncated)
hello-nf-core/solutions/core-hello-part5/main.nf(truncated)
hello-nf-core/solutions/core-hello-part5/modules/local/convertToUpper.nf(truncated)
hello-nf-core/solutions/core-hello-part5/modules/local/cowpy.nf(truncated)
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)
hello-nf-core/solutions/core-hello-part5/workflows/hello.nf(truncated)
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hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nextflow_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfcore_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
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side-quests/solutions/essential_scripting_patterns/collect.nf(truncated)
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side-quests/solutions/nf-core/myorg-myfirstpipeline/modules/nf-core/multiqc/tests/nextflow.config(truncated)
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side-quests/solutions/nf-core/myorg-myfirstpipeline/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config(truncated)
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side-quests/solutions/nf-core/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
side-quests/solutions/nf-core/myorg-myfirstpipeline/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
side-quests/solutions/nf-core/myorg-myfirstpipeline/workflows/myfirstpipeline.nf(truncated)
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side-quests/solutions/plugin_development/nextflow.config(truncated)
side-quests/solutions/splitting_and_grouping/main.nf(truncated)
side-quests/sol...*[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 30 commits January 9, 2026 13:05
@pinin4fjords @claude
Fix review issues in plugin development side quest
59bc6c4 
- Replace implicit 'it' with explicit parameter in summary example
- Update section references from 3-10 to 3-11 throughout
- Add operators and trace observers to development checklist
- Change "publish" to "distribute" in learning goals

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords
Fix a highlight
5bbd0af
@pinin4fjords
Fix a highlight
2191cda
@pinin4fjords @claude
Add explanation for operator code in section 8.2
f249512 
- Fix hl_lines to highlight correct lines (24-29 for imports, 62-73 for operator)
- Add line-by-line breakdown explaining DataflowHelper, callbacks, and Channel.STOP

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add explanations for config changes in section 9.2
f722695 
- Fix malformed hl_lines (24-16 -> 24-26)
- Add key changes explanation for TaskCounterObserver (verbose flag, constructor, conditional print)
- Add explanation for NfGreetingFactory config reading

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords
update solutions
980258d
@pinin4fjords
Re-fix highlight
a5db0b0
@pinin4fjords
Merge branch 'custom-training-advanced-topics' of github.com:nextflow…
eebc4b3 
…-io/training into custom-training-advanced-topics
@pinin4fjords
Fix a highlight
716f61a
@pinin4fjords
Reset starting files
8660cad
@pinin4fjords @claude
Fix section 0 heading structure and config syntax consistency
c9ac81c 
- Convert section 0's #### headings to numbered ### subsections (0.1-0.6)
  to match the style used throughout the rest of the document
- Use consistent dot notation for taskCounter.verbose in section 9.2
  to match section 9.3's style

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Clarify publishDir limitations in workflow outputs side quest
312af75 
Improved the explanation to acknowledge that publishDir can be configured
via processes or config selectors (withName/withLabel), and explained
what a manifest is for readers unfamiliar with the term.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add conceptual introduction to workflow outputs approach
21f040a 
Explains the fundamental shift: with publishDir, processes handle their
own publishing; with workflow outputs, publishing moves to the workflow
level. This provides context before diving into syntax details.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords
Highlight fixes
b4dc7cc
@pinin4fjords @claude
Add guidance for correct hl_lines usage in code blocks
35773ce 
- CLAUDE.md: Add detailed explanation that hl_lines is snippet-relative,
  with worked example showing how to count lines (including blanks)
- new-lesson.md: Add concise instruction for setting hl_lines correctly
- New check-highlights skill: Verification tool for reviewing highlight
  line numbers in existing documentation

Key points reinforced: count from line 1 of snippet, blank lines count,
hl_lines is independent of linenums.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Restructure workflow outputs side quest for clearer teaching
4d8d9e2 
- Section 1 now starts with processes that already have metadata tuples
  (greeting and language), so adding tuples isn't conflated with the
  workflow output syntax
- Section 2 now only teaches removing publishDir and adding the workflow
  output syntax - a single focused concept
- Updated starter files (main.nf, modules/greetings.nf) to match docs
- Fixed hl_lines values that were off-by-one

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add main: block requirement when using publish: section
788bcae 
When a workflow uses a publish: section, the workflow content must be
placed in a main: block. Updated the After example and explanation.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix hl_lines to not highlight closing brace
a98d753 
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add Before/After comparison for output block section
f12d5cc 
Shows the complete main.nf file with and without the output block,
making the change clearer and more consistent with other sections.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add nextflow.preview.output flag for older Nextflow version
29c2783 
The training environment uses an older Nextflow version that requires
this flag. Added note explaining this is not needed in 25.10+.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add main: block to workflow outputs solution
45b5b63 
The solution was missing the required main: block when using publish:

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix feature flag location - must be in script, not config
2d072ce 
The nextflow.preview.output flag must be in the script file, not
nextflow.config. Updated documentation and solution to add the flag
at the top of main.nf when the output block is added.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Add feature flag to starter workflow
5de07c0 
Include nextflow.preview.output in the starter main.nf so users don't
need to add it manually. Updated all code blocks in documentation to
include the flag consistently.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix index file example output to match reality
ddbc3db 
- CSV output has no header row (tuples don't have field names)
- Paths are absolute, not relative
- Clarified tip about using maps for named fields

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Use [meta, file] tuple pattern throughout workflow outputs tutorial
0ae083b 
- Refactored to use nf-core community standard [meta, file] tuples
- meta map contains id and language fields
- Updated all code examples to use meta.language for dynamic paths
- Changed index format from CSV to JSON (works better with meta maps)
- JSON properly expands meta maps to objects with named fields
- Removed outdated tip about using maps (now using them from the start)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Update example outputs with real results
0c7b5e4 
- JSON index shows all 5 greetings with proper /workspaces paths
- File listing sorted alphabetically to match real output

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Fix hl_lines in workflow outputs section 2.3 Before block
57683ae 
Line 25 was the process declaration, not the second publishDir which
is on line 27.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Remove custom operators and factories from plugin development tutorial
78a418c 
Based on feedback from @bentsherman: custom operators/factories are in a
precarious position for future type checking support, and nearly every
example would have been better as a custom function.

Changes:
- Remove Section 8 (Custom operators and factories) entirely
- Remove Section 10.1 (Channel factories)
- Renumber sections 9-11 to 8-10
- Update all references to operators/factories throughout
- Update code examples to use functions instead of shoutAll operator
- Keep focus on functions and trace observers as the key extension types

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Update plugin development solution to remove operator usage
4efb6ab 
Remove shoutAll operator from main.nf solution, use reverseGreeting
function instead to match the updated tutorial content.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
@pinin4fjords @claude
Clarify extensionPoints description
e00b7f0 
Change "functions, factories, etc." to "functions, observers, etc." to
avoid confusion with channel factories (which were removed).

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