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Improvements to Side Quest: Metadata #748

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@vdauwera
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@vdauwera vdauwera commented Dec 4, 2025 •
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Based on 2025 teaching experience

Mainly improvements to instructions and consistent formatting. More detail across the board. Reordering section 3 to make more intuitive sense (see commit notes)

@vdauwera vdauwera added this to the Side Quests vol 1 milestone Dec 4, 2025
@vdauwera vdauwera self-assigned this Dec 4, 2025
@vdauwera vdauwera added improve New feature or request side quests labels Dec 4, 2025
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github-actions bot commented Dec 4, 2025 •
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Nextflow linting complete!

❌ 5 files had 33 errors
✅ 150 files had no errors
🔧 135 files would be changed by auto-formatting

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

View all 33 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/composable-hello/hello.nf:11:1 Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/composable-hello/modules/sayHello.nf'
Error hello-nf-core/solutions/composable-hello/hello.nf:12:1 Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/composable-hello/modules/convertToUpper.nf'
Error hello-nf-core/solutions/composable-hello/hello.nf:13:1 Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/composable-hello/modules/collectGreetings.nf'
Error hello-nf-core/solutions/composable-hello/hello.nf:14:1 Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/composable-hello/modules/cowpy.nf'
Error hello-nf-core/solutions/composable-hello/hello.nf:24:5 sayHello is not defined
Error hello-nf-core/solutions/composable-hello/hello.nf:27:5 convertToUpper is not defined
Error hello-nf-core/solutions/composable-hello/hello.nf:27:20 sayHello is not defined
Error hello-nf-core/solutions/composable-hello/hello.nf:30:5 collectGreetings is not defined
Error hello-nf-core/solutions/composable-hello/hello.nf:30:22 convertToUpper is not defined
Error hello-nf-core/solutions/composable-hello/hello.nf:33:5 cowpy is not defined
Error hello-nf-core/solutions/composable-hello/hello.nf:33:11 collectGreetings is not defined
Error hello-nf-core/solutions/composable-hello/hello.nf:36:20 cowpy is not defined
Error hello-nf-core/solutions/core-hello-part2/nextflow.config:154:17 Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/core-hello-part2/conf/test_full.config'
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:1:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/validate_name.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:2:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/say_hello.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:3:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/timestamp_greeting.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:11:24 VALIDATE_NAME is not defined
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:12:24 SAY_HELLO is not defined
Error side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:13:26 TIMESTAMP_GREETING is not defined
Error side-quests/solutions/workflows_of_workflows/workflows/transform.nf:1:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/say_hello_upper.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/transform.nf:2:1 Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/reverse_text.nf'
Error side-quests/solutions/workflows_of_workflows/workflows/transform.nf:10:20 SAY_HELLO_UPPER is not defined
Error side-quests/solutions/workflows_of_workflows/workflows/transform.nf:11:23 REVERSE_TEXT is not defined
View formatting changes
FileDiff
hello-nextflow/solutions/1-hello-world/hello-world-3.nf
View 
@@ -8,7 +8,7 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     output:
-        path 'output.txt'
+    path 'output.txt'
 
     script:
     """
hello-nextflow/solutions/1-hello-world/hello-world-4.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path 'output.txt'
+    path 'output.txt'
 
     script:
     """
-    echo '$greeting' > output.txt
+    echo '${greeting}' > output.txt
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path 'output.txt'
+    path 'output.txt'
 
     script:
     """
-    echo '$greeting' > output.txt
+    echo '${greeting}' > output.txt
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf
View 
@@ -8,14 +8,14 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf
View 
@@ -8,14 +8,14 @@ process convertToUpper {
     publishDir 'results', mode: 'copy'
 
     input:
-        path input_file
+    path input_file
 
     output:
-        path "UPPER-${input_file}"
+    path "UPPER-${input_file}"
 
     script:
     """
-    cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
+    cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf
View 
@@ -8,15 +8,15 @@ process collectGreetings {
     publishDir 'results', mode: 'copy'
 
     input:
-        path input_files
-        val batch_name
+    path input_files
+    val batch_name
 
     output:
-        path "COLLECTED-${batch_name}-output.txt" , emit: outfile
-        val count_greetings , emit: count
+    path "COLLECTED-${batch_name}-output.txt", emit: outfile
+    val count_greetings, emit: count
 
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf
View 
@@ -15,8 +15,8 @@ workflow {
 
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.greeting)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
 
     // emit a greeting
     sayHello(greeting_ch)
@@ -28,5 +28,5 @@ workflow {
     collectGreetings(convertToUpper.out.collect(), params.batch)
 
     // emit a message about the size of the batch
... (truncated)
hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf
View 
@@ -6,15 +6,15 @@ process collectGreetings {
     publishDir 'results', mode: 'copy'
 
     input:
-        path input_files
-        val batch_name
+    path input_files
+    val batch_name
 
     output:
-        path "COLLECTED-${batch_name}-output.txt" , emit: outfile
-        val count_greetings , emit: count
+    path "COLLECTED-${batch_name}-output.txt", emit: outfile
+    val count_greetings, emit: count
 
... (truncated)
hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf
View 
@@ -8,13 +8,13 @@ process convertToUpper {
     publishDir 'results', mode: 'copy'
 
     input:
-        path input_file
+    path input_file
 
     output:
-        path "UPPER-${input_file}"
+    path "UPPER-${input_file}"
 
     script:
     """
-    cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
+    cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
... (truncated)
hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf
View 
@@ -8,13 +8,13 @@ process sayHello {
     publishDir 'results', mode: 'copy'
 
     input:
-        val greeting
+    val greeting
 
     output:
-        path "${greeting}-output.txt"
+    path "${greeting}-output.txt"
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
... (truncated)
hello-nextflow/solutions/5-hello-containers/modules/cowpy.nf
View 
@@ -8,14 +8,14 @@ process cowpy {
     container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273'
 
     input:
-        path input_file
-        val character
+    path input_file
+    val character
 
     output:
-        path "cowpy-${input_file}"
+    path "cowpy-${input_file}"
 
     script:
     """
... (truncated)
hello-nextflow/solutions/6-hello-config/modules/cowpy.nf
View 
@@ -9,14 +9,14 @@ process cowpy {
     conda 'conda-forge::cowpy==1.1.5'
 
     input:
-        path input_file
-        val character
+    path input_file
+    val character
 
     output:
-        path "cowpy-${input_file}"
+    path "cowpy-${input_file}"
 
     script:
     """
... (truncated)
hello-nf-core/solutions/composable-hello/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/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 
@@ -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-nf-core/solutions/core-hello-part2/modules/local/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-nf-core/solutions/core-hello-part2/modules/local/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/core-hello-part2/modules/local/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-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf
View 
@@ -8,13 +8,13 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-schema'
-include { samplesheetToList         } from 'plugin/nf-schema'
-include { paramsHelp                } from 'plugin/nf-schema'
-include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap } from 'plugin/nf-schema'
+include { samplesheetToList } from 'plugin/nf-schema'
+include { paramsHelp } from 'plugin/nf-schema'
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
View 
@@ -10,9 +10,9 @@
 
 workflow UTILS_NEXTFLOW_PIPELINE {
     take:
-    print_version        // boolean: print version
-    dump_parameters      // boolean: dump parameters
-    outdir               //    path: base directory used to publish pipeline results
+    print_version // boolean: print version
+    dump_parameters // boolean: dump parameters
+    outdir //    path: base directory used to publish pipeline results
     check_conda_channels // boolean: check conda channels
 
     main:
@@ -72,10 +72,10 @@ def getWorkflowVersion() {
 //
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
View 
@@ -1,9 +1,9 @@
 manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
+    name = 'nextflow_workflow'
+    author = """nf-core"""
+    homePage = 'https://127.0.0.1'
+    description = """Dummy pipeline"""
     nextflowVersion = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+    version = '9.9.9'
+    doi = 'https://doi.org/10.5281/zenodo.5070524'
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
View 
@@ -125,12 +125,12 @@ def paramsSummaryMultiqc(summary_params) {
         }
 
     def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
-    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
-    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text     += "plot_type: 'html'\n"
-    yaml_file_text     += "data: |\n"
-    yaml_file_text     += "${summary_section}"
+    yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text += "plot_type: 'html'\n"
+    yaml_file_text += "data: |\n"
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
View 
@@ -1,9 +1,9 @@
 manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+    name = 'nextflow_workflow'
+    author = """nf-core"""
+    homePage = 'https://127.0.0.1'
+    description = """Dummy pipeline"""
+    nextflowVersion = '!>=23.04.0'
+    version = '9.9.9'
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf
View 
@@ -2,30 +2,25 @@
 // Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
 //
 
-include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { paramsSummaryLog } from 'plugin/nf-schema'
 include { validateParameters } from 'plugin/nf-schema'
-include { paramsHelp         } from 'plugin/nf-schema'
+include { paramsHelp } from 'plugin/nf-schema'
 
 workflow UTILS_NFSCHEMA_PLUGIN {
-
     take:
-    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
-    validate_params     // boolean:  validate the parameters
... (truncated)
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vdauwera added 12 commits December 5, 2025 14:45
@vdauwera
improvements up to 2.3
815362a
@vdauwera
Finished improvements to part 2 (big explanation for map merging)
e75d9d4
@vdauwera
remove titles from small code boxes if not informative
206641f
@vdauwera
Reorder section 3
9acb972 
More logical to provide the process as a module and reorder the steps so we customize the character right off the bat (shows passing the metadata as an argument) then fiddling with the output directories as a way to use metadata inside the process (though we'll have to think how that changes once we introduce workflow-level outputs, maybe switch to filename customization)
@vdauwera
header number fix + couple of TODO notes
3dd9c8a
@vdauwera
refactored part 3 to streamline
b2975eb
@vdauwera
fix header number format
250652b
@vdauwera
minor fixes
93caf65
@vdauwera
minor fixes
9fbad39
@vdauwera
Fix troubleshooting bits based on testing
1529319
@vdauwera
headerrrrrrr fix
abfddce
@vdauwera
formetting fixes
ba2b53f
@vdauwera vdauwera marked this pull request as ready for review December 26, 2025 18:25
@vdauwera vdauwera mentioned this pull request Dec 26, 2025
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vdauwera commented Dec 26, 2025 •
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This is ready for review. I made some important changes to section 3 to streamline and explain more clearly what was going on.

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