Add plugin development side quest, restructure side quests for multi-part courses

[pinin4fjords]

Summary

Adds a Plugin Development side quest (6 progressive lessons on Nextflow plugin development) and restructures all side quests to support multi-part courses consistently.

Plugin Development course

• Part 1: Using existing plugins (nf-hello, nf-schema, nf-co2footprint), including config demos
• Part 2: Scaffolding a plugin project with nextflow plugin create
• Part 3: Custom @function methods (reverseGreeting, decorateGreeting)
• Part 4: Spock unit testing
• Part 5: TraceObserver lifecycle events (GreetingObserver, TaskCounterObserver)
• Part 6: Configuration (navigate() for reading, ConfigScope for declaring)

Written for Nextflow 25.10.2 using the plugin Gradle plugin (io.nextflow.nextflow-plugin 1.0.0-beta.10) and config.spec.* API.

Side quests restructure

• Each side quest now lives in its own subdirectory (side_quests/questname/index.md), matching the nf4_science pattern and allowing any quest to expand into multiple pages in the future
• Single-page quests remain direct nav entries (no extra click); multi-part courses like Plugin Development get a named subsection
• Updated all cross-references between side quest pages for new paths
• Added Plugin Development course box to the side quests index page

Other changes

• .editorconfig: Makefile tab rule for plugin solutions
• .gitignore: .gradle/ ignore for plugin builds
• .pre-commit-config.yaml: Excludes for template-generated files (COPYING, gradlew)
• .prettierignore: Exclude COPYING files in plugin solutions
• docs/en/docs/envsetup/02_local.md: Java 21 requirement note for plugin development

Test plan

• Preview locally with MkDocs
• Tutorial walkthrough tested for Parts 1-6 (Mode A, learner simulation in Docker)
• All solutions build and run correctly
• All solutions pass -resume caching
• Validation checks pass on all 6 lesson files (headings, hl_lines, inline code, writing style)
• Nav structure verified via deploy preview

Follow-up issues

• Plugin dev: consider removing mermaid class diagram in Part 2 #921 - Consider removing/moving mermaid class diagram in Part 2
• Plugin dev: tighten config section (Part 6) #922 - Tighten config section (Part 6)
• Plugin dev: add meaningful TraceObserver data usage example #923 - Add meaningful TraceObserver data usage example (Part 5)
• Plugin dev: coordinate with Nextflow docs to avoid content overlap #925 - Coordinate with Nextflow docs to avoid content overlap

🤖 Generated with Claude Code

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[github-actions]

Nextflow linting complete!

✅ 171 files had no errors
🔧 127 files would be changed by auto-formatting

View formatting changes

File	Diff
hello-nextflow/solutions/1-hello-world/hello-world-2.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - output: path 'output.txt'
hello-nextflow/solutions/1-hello-world/hello-world-3.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -29,7 +28,7 @@ workflow { main: // create a channel for inputs greeting_ch = channel.of('Hello Channels!') - .view() + .view() // emit a greeting ... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -29,7 +28,7 @@ workflow { main: // create a channel for inputs greeting_ch = channel.of('Hello', 'Bonjour', 'Holà') - .view() + .view() // emit a greeting ... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -28,12 +27,12 @@ workflow { main: // declare an array of input greetings - greetings_array = ['Hello','Bonjour','Holà'] + greetings_array = ['Hello', 'Bonjour', 'Holà'] // create a channel for inputs ... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -29,11 +28,11 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .view { csv -> "Before splitCsv: $csv" } - .splitCsv() - .view { csv -> "After splitCsv: $csv" } ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf	View @@ -7,7 +7,6 @@ include { sayHello } from './modules/sayHello.nf' * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file @@ -24,7 +23,6 @@ process convertToUpper { * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files ... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf	View @@ -8,7 +8,6 @@ include { convertToUpper } from './modules/convertToUpper.nf' * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name @@ -38,8 +37,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() ... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf	View @@ -18,8 +18,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) // convert the greeting to uppercase
hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf	View @@ -2,7 +2,6 @@ * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name
hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf	View @@ -2,7 +2,6 @@ * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file
hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf	View @@ -2,7 +2,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf	View @@ -20,8 +20,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) // convert the greeting to uppercase
hello-nextflow/solutions/5-hello-containers/modules/collectGreetings.nf	View @@ -2,7 +2,6 @@ * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name
hello-nextflow/solutions/5-hello-containers/modules/convertToUpper.nf	View @@ -2,7 +2,6 @@ * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file
hello-nextflow/solutions/5-hello-containers/modules/sayHello.nf	View @@ -2,7 +2,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/6-hello-config/hello-config.nf	View @@ -20,8 +20,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) // convert the greeting to uppercase
hello-nextflow/solutions/6-hello-config/modules/collectGreetings.nf	View @@ -2,7 +2,6 @@ * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name
hello-nextflow/solutions/6-hello-config/modules/convertToUpper.nf	View @@ -2,7 +2,6 @@ * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file
hello-nextflow/solutions/6-hello-config/modules/sayHello.nf	View @@ -2,7 +2,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/6-hello-config/nextflow.config	View @@ -6,7 +6,7 @@ conda.enabled = true */ process { memory = 1.GB - withName: 'cowpy' { + withName: cowpy { memory = 2.GB cpus = 2 } @@ -32,11 +32,7 @@ profiles { univ_hpc { process.executor = 'slurm' conda.enabled = true - process.resourceLimits = [ - memory: 750.GB, ... (truncated)
hello-nf-core/solutions/composable-hello/hello.nf	View @@ -14,9 +14,7 @@ include { collectGreetings } from './modules/collectGreetings.nf' include { cowpy } from './modules/cowpy.nf' workflow HELLO { - take: - // channel of greetings greeting_ch main:
hello-nf-core/solutions/composable-hello/main.nf	View @@ -9,12 +9,12 @@ params.greeting = 'greetings.csv' workflow { // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.greeting) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // call the imported workflow on the channel of greetings HELLO(greeting_ch) // view the outputs emitted by the workflow - HELLO.out.view { output -> "Output: $output" } + HELLO.out.view { output -> "Output: ${output}" } ... (truncated)
hello-nf-core/solutions/composable-hello/modules/collectGreetings.nf	View @@ -10,8 +10,8 @@ process collectGreetings { val batch_name output: - path "COLLECTED-${batch_name}-output.txt" , emit: outfile - val count_greetings , emit: count + path "COLLECTED-${batch_name}-output.txt", emit: outfile + val count_greetings, emit: count script: count_greetings = input_files.size()
hello-nf-core/solutions/composable-hello/modules/convertToUpper.nf	View @@ -13,6 +13,6 @@ process convertToUpper { script: """ - cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' """ }
hello-nf-core/solutions/composable-hello/modules/cowpy.nf	View @@ -15,6 +15,6 @@ process cowpy { script: """ - cat $input_file | cowpy -c "$character" > cowpy-${input_file} + cat ${input_file} | cowpy -c "${character}" > cowpy-${input_file} """ }
hello-nf-core/solutions/composable-hello/modules/sayHello.nf	View @@ -13,6 +13,6 @@ process sayHello { script: """ - echo '$greeting' > '$greeting-output.txt' + echo '${greeting}' > '${greeting}-output.txt' """ }
hello-nf-core/solutions/core-hello-part2/conf/base.config	View @@ -11,13 +11,13 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { 1 * task.attempt } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } - maxRetries = 1 - maxErrors = '-1' + maxRetries = 1 ... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/modules.config	View @@ -12,10 +12,5 @@ process { - publishDir = [ - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - + publishDir = [path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] }
hello-nf-core/solutions/core-hello-part2/conf/test.config	View @@ -11,21 +11,17 @@ */ process { - resourceLimits = [ - cpus: 2, - memory: '4.GB', - time: '1.h' - ] + resourceLimits = [cpus: 2, memory: '4.GB', time: '1.h'] } params { - config_profile_name = 'Test profile' + config_profile_name = 'Test profile' ... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/test_full.config	View @@ -11,7 +11,7 @@ */ params { - config_profile_name = 'Full test profile' + config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test
hello-nf-core/solutions/core-hello-part2/main.nf	View @@ -13,9 +13,9 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { HELLO } from './workflows/hello' +include { HELLO } from './workflows/hello' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_hello_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -26,7 +26,6 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hell // WORKFLOW: Run main analysis pipeline depending on type of input // ... (truncated)
hello-nf-core/solutions/core-hello-part2/modules/local/collectGreetings.nf	View @@ -10,8 +10,8 @@ process collectGreetings { val batch_name output: - path "COLLECTED-${batch_name}-output.txt" , emit: outfile - val count_greetings , emit: count + path "COLLECTED-${batch_name}-output.txt", emit: outfile + val count_greetings, emit: count script: count_greetings = input_files.size()
hello-nf-core/solutions/core-hello-part2/modules/local/convertToUpper.nf	View @@ -13,6 +13,6 @@ process convertToUpper { script: """ - cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' """ }
hello-nf-core/solutions/core-hello-part2/modules/local/cowpy.nf	View @@ -7,14 +7,14 @@ process cowpy { conda 'conda-forge::cowpy==1.1.5' input: - path input_file - val character + path input_file + val character output: - path "cowpy-${input_file}" + path "cowpy-${input_file}" script: """ ... (truncated)
hello-nf-core/solutions/core-hello-part2/modules/local/sayHello.nf	View @@ -13,6 +13,6 @@ process sayHello { script: """ - echo '$greeting' > '$greeting-output.txt' + echo '${greeting}' > '${greeting}-output.txt' """ }
hello-nf-core/solutions/core-hello-part2/nextflow.config	View @@ -11,30 +11,30 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options - input = null + input = null // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - monochrome_logs = false - help = false - help_full = false - show_hidden = false - version = false ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf	View @@ -8,13 +8,13 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { samplesheetToList } from 'plugin/nf-schema' -include { paramsHelp } from 'plugin/nf-schema' -include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/main.nf	View @@ -10,9 +10,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { take: - print_version // boolean: print version - dump_parameters // boolean: dump parameters - outdir // path: base directory used to publish pipeline results + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results check_conda_channels // boolean: check conda channels main: @@ -72,10 +72,10 @@ def getWorkflowVersion() { // ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config	View @@ -1,9 +1,9 @@ manifest { - name = 'nextflow_workflow' - author = """nf-core""" - homePage = 'https://127.0.0.1' - description = """Dummy pipeline""" + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" nextflowVersion = '!>=23.04.0' - version = '9.9.9' - doi = 'https://doi.org/10.5281/zenodo.5070524' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf	View @@ -125,12 +125,12 @@ def paramsSummaryMultiqc(summary_params) { } def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config	(truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf	(truncated)
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[bentsherman]

@pinin4fjords I would completely remove any mention of creating custom factories / operators. Nearly every example of a custom factory / operator that I see in the wild would have been better as a custom function, and they are currently in a precarious position in terms of future type checking support.

Otherwise, it looks like the right idea. Custom functions and trace observers are by far the most important to cover. Custom executors and filesystems are also powerful but way more complicated -- if you try to cover them at all, I would put them in a separate tutorial.

[pinin4fjords]

@pinin4fjords I would completely remove any mention of creating custom factories / operators. Nearly every example of a custom factory / operator that I see in the wild would have been better as a custom function, and they are currently in a precarious position in terms of future type checking support.

Otherwise, it looks like the right idea. Custom functions and trace observers are by far the most important to cover. Custom executors and filesystems are also powerful but way more complicated -- if you try to cover them at all, I would put them in a separate tutorial.

Thanks @bentsherman !

[adamrtalbot]

Just reviewed the "using plugins" section.

• Let's make it shorter and tighter, it's verbose and wordy.
• Focus on how plugins extend Nextflow functionality rather than sharing code
• Keep it simple and explain it one way and only one way.

[bentsherman]

For section 8 on custom plugin configuration, it might be worth mentioning that you can define your custom config as a proper class with some annotations, so that the Nextflow linter and language server can recognize it.

But this tutorial is already pretty long and I've already documented it here, so you could just add a blurb with a link to these docs.

[pinin4fjords]

Complete list of changes from transcript analysis

After reviewing the transcript of the live delivery session, the following improvements were made across multiple commits:

Structural improvements

• Progressive Section 4: Now adds functions one at a time (reverseGreeting → decorateGreeting → friendlyGreeting) instead of all three at once
• Progressive Section 7.2: Observer built in 3 steps (minimal observer → register it → add counting logic)
• Progressive Section 8.3: Intentionally leads learners through the "variable not declared" error as a teaching moment, then shows the fix
• Class relationship diagram: Added mermaid diagram in Section 3.2 showing how plugin classes relate

"Run it first" pedagogy

• Added step to run random_id_example.nf before examining code (Section 2.6)
• Added step to run main.nf before modifying it (Section 6.2)
• This matches the teaching pattern of "see it work, then understand how"

Clearer transitions

• Section 6.1: Fixed awkward transition from nf-hello to nf-greeting config - now explicitly shows replacing one with the other
• Added note explaining random_id_example.nf won't work after config change (and that's OK)

Additional context and reassurance

• Local vs published plugins: Added info box explaining where local plugins are stored ($NXF_HOME/plugins/)
• Registry browsing exercise: Added exercise to explore plugins.nextflow.io
• Java expertise reassurance: Enhanced prerequisites to reassure learners they don't need Java expertise
• Common runtime issues: Added warning box with troubleshooting tips
• -ansi-log false tip: Enhanced explanation of why this flag is needed for observer output

Configuration section enhancements

• Type-safe config example: Added collapsible advanced example showing @ConfigScope annotations
• Expected output blocks: Added more output examples so learners know what to expect

Accuracy fixes (this commit)

• Java version: 17 → 21 (matches training environment)
• Error line numbers: "line 7" → "line 30" (matches actual compiler output)

All changes verified by running complete tutorial walkthrough in Docker container.

[adamrtalbot]

Mostly good but needs some tightening up at points. I think it hits all the right points so the rough structure is good.

The only thing I can see which is missing is using a TraceObserver and reading one of the items that originates from it, e.g. onPublish -> use file path for something.

[adamrtalbot]

The config section is s still a bit weak and could be tightened but the rest is pretty solid now.