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Add Types and Records side quest (Nextflow 26.10) - #997

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Add Types and Records side quest (Nextflow 26.10)#997
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types-and-records-side-quest

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@pinin4fjords

@pinin4fjords pinin4fjords commented Oct 5, 2026

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Summary

Adds a new side quest, Types and Records, in the "Deep Dives into Dataflow" group after Metadata. It teaches Nextflow's static typing through one evolving greeting pipeline:

  • The problem: a collaborator's samplesheet renames a column. The untyped pipeline still succeeds, but it quietly writes null, Alice!.
  • Static typing: the nextflow.enable.types flag, typed process inputs and outputs, and the one-file rule for mixing typed and legacy definitions.
  • Records:
    • Record types in a shared types.nf.
    • A Channel<Person> param that loads and validates the samplesheet. The bad sheet is rejected at load and names the missing field.
    • + to carry metadata through, the record version of meta + [...].
    • Destructured inputs to select a subset of fields.
  • Typed workflows: take:/emit: with record types, structural matching, Channel vs Value, and named emits read as fields.
  • Catching mistakes: nextflow lint catches a misspelled field and a wrongly typed argument before anything runs.

The PR also adds the nav entry, a row in the side-quest index, and a forward pointer from the end of the Metadata side quest. It is the prerequisite for Part 2 of the upcoming Composing Pipelines course.

Requires Nextflow 26.10

The quest targets Nextflow 26.10. Channel<T> params loaded from samplesheets, and the type checks shown, are not in 26.04. The page carries one "requires Nextflow 26.10 or later" note and no comparisons between versions.

Draft until 26.10 is released. Before merging:

  • Bump NXF_VER to the 26.10 release in the devcontainer files.
  • Re-capture console output on 26.10. It is currently captured on a 26.09 edge build of the composition branch.
  • Remove the TODO(26.10) comment at the top of the page.

Testing

  • Independent learner walkthroughs (run-tutorial Mode A) in the training container with the 26.10 stand-in build: every Before block matches, every output matches, and the built code is identical to the solution.
  • The solution runs, resumes fully cached, and lints clean.
  • Heading check, prettier, check-highlights, check-inline-code, and an English mkdocs build with no warnings.
  • Three rounds of adversarial pedagogy review, with their findings addressed.

🤖 Generated with Claude Code

pinin4fjords and others added 2 commits October 5, 2026 17:57
@pinin4fjords @claude
feat(side-quests): add Types and Records side quest [skip ci]
0197b56 
New side quest teaching static typing on Nextflow 26.04: the
nextflow.enable.types flag, typed process inputs and outputs, records
(literals, record types, destructured inputs, merging with +), typed
workflows with Channel<T> and Value<T>, and using nextflow lint to catch
interface mistakes. Built around one evolving greeting pipeline whose
untyped meta maps silently produce wrong output when a samplesheet
column is renamed.

Adds the nav entry, the side quest index row and a forward pointer from
the metadata side quest.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@pinin4fjords @claude
feat(side-quests): target Nextflow 26.10 in Types and Records
26ca5f6 
Rework the side quest after review and learner walkthroughs:

- Load the samplesheet through a Channel<Person> param, so a renamed
  column is rejected at load time with the missing field named, and
  have the learner fix the sheet and rerun from the cache.
- Keep record types in a shared types.nf, carry metadata through
  outputs with `+` (the record form of meta + [...]), and contrast it
  with destructured inputs that select a subset of fields.
- Explain structural record matching, typed take:/emit: as the
  workflow's documented interface, and Channel vs Value.
- Show nextflow lint catching a misspelled field and a wrongly typed
  argument before anything runs.
- Explain the type-check warning seen partway through the migration.
- Trim to fit the one-hour estimate, and replace version-specific
  caveats with a single note that the quest requires Nextflow 26.10.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Nextflow linting complete!

⚠️ 32 files had 45 warnings
✅ 189 files had no errors
🔧 134 files would be changed by auto-formatting

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

View all 45 issues
Type Location Message
Warning nfcore-build/solutions/composable-hello/hello.nf:36:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part1/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part1/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part1/workflows/hello.nf:68:17 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part2/workflows/hello.nf:45:55 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part2/workflows/hello.nf:77:17 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-part3/modules/local/cowpy/main.nf:30:9 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part3/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part3/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part3/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part3/workflows/hello.nf:74:17 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-part4/modules/local/cowpy/main.nf:30:9 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-part4/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part4/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part4/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-part4/workflows/hello.nf:74:17 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-start/subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-start/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-start/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5 Emit name should be omitted when there is only one emit
Warning nfcore-build/solutions/core-hello-start/workflows/hello.nf:18:5 Parameter was not used -- prefix with _ to suppress warning
Warning nfcore-build/solutions/core-hello-start/workflows/hello.nf:45:9 Variable was declared but not used
Warning nfcore-build/solutions/core-hello-start/workflows/hello.nf:54:5 Emit name should be omitted when there is only one emit
Warning side-quests/solutions/debugging/buggy_workflow.nf:91:44 Implicit closure parameter is deprecated, declare an explicit parameter instead
Warning side-quests/solutions/essential_scripting_patterns/main.nf:59:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/essential_scripting_patterns/main.nf:63:53 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/essential_scripting_patterns/main.nf:68:5 Variable was declared but not used
Warning side-quests/solutions/essential_scripting_patterns/main.nf:69:5 Variable was declared but not used
Warning side-quests/solutions/metadata/1.2/main.nf:5:5 Variable was declared but not used
Warning side-quests/solutions/splitting_and_grouping/main.nf:11:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/splitting_and_grouping/main.nf:14:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/splitting_and_grouping/main.nf:29:5 Variable was declared but not used
Warning side-quests/solutions/working_with_files/6/main.nf:10:43 Variable was declared but not used
Warning side-quests/solutions/working_with_files/6/main.nf:30:22 Parameter was not used -- prefix with _ to suppress warning
View formatting changes
FileDiff
hello-nextflow/solutions/1-hello-world/hello-world-2.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     output:
     path 'output.txt'
hello-nextflow/solutions/1-hello-world/hello-world-3.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -29,7 +28,7 @@ workflow {
     main:
     // create a channel for inputs
     greeting_ch = channel.of('Hello Channels!')
-                        .view()
+        .view()
     // emit a greeting
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -29,7 +28,7 @@ workflow {
     main:
     // create a channel for inputs
     greeting_ch = channel.of('Hello', 'Bonjour', 'Hola')
-                        .view()
+        .view()
     // emit a greeting
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -28,12 +27,12 @@ workflow {
 
     main:
     // declare an array of input greetings
-    greetings_array = ['Hello','Bonjour','Hola']
+    greetings_array = ['Hello', 'Bonjour', 'Hola']
     // create a channel for inputs
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -29,11 +28,11 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .view { csv -> "Before splitCsv: $csv" }
-                        .splitCsv()
-                        .view { csv -> "After splitCsv: $csv" }
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf
View 
@@ -7,7 +7,6 @@ include { sayHello } from './modules/sayHello.nf'
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
 
@@ -24,7 +23,6 @@ process convertToUpper {
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf
View 
@@ -8,7 +8,6 @@ include { convertToUpper } from './modules/convertToUpper.nf'
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
@@ -38,8 +37,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf
View 
@@ -18,8 +18,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
     // emit a greeting
     sayHello(greeting_ch)
     // convert the greeting to uppercase
hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf
View 
@@ -2,7 +2,6 @@
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf
View 
@@ -2,7 +2,6 @@
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf
View 
@@ -2,7 +2,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf
View 
@@ -20,8 +20,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
     // emit a greeting
     sayHello(greeting_ch)
     // convert the greeting to uppercase
hello-nextflow/solutions/5-hello-containers/modules/collectGreetings.nf
View 
@@ -2,7 +2,6 @@
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
hello-nextflow/solutions/5-hello-containers/modules/convertToUpper.nf
View 
@@ -2,7 +2,6 @@
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
hello-nextflow/solutions/5-hello-containers/modules/sayHello.nf
View 
@@ -2,7 +2,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/6-hello-config/hello-config.nf
View 
@@ -20,8 +20,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
     // emit a greeting
     sayHello(greeting_ch)
     // convert the greeting to uppercase
hello-nextflow/solutions/6-hello-config/modules/collectGreetings.nf
View 
@@ -2,7 +2,6 @@
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
hello-nextflow/solutions/6-hello-config/modules/convertToUpper.nf
View 
@@ -2,7 +2,6 @@
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
hello-nextflow/solutions/6-hello-config/modules/sayHello.nf
View 
@@ -2,7 +2,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/6-hello-config/nextflow.config
View 
@@ -6,7 +6,7 @@ conda.enabled = true
 */
 process {
     memory = 1.GB
-    withName: 'cowpy' {
+    withName: cowpy {
         memory = 2.GB
         cpus = 2
     }
@@ -32,11 +32,7 @@ profiles {
     univ_hpc {
         process.executor = 'slurm'
         conda.enabled = true
-        process.resourceLimits = [
-            memory: 750.GB,
... (truncated)
nfcore-build/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:
nfcore-build/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)
nfcore-build/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()
nfcore-build/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}
     """
 }
nfcore-build/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}
     """
 }
nfcore-build/solutions/composable-hello/modules/sayHello.nf
View 
@@ -13,6 +13,6 @@ process sayHello {
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
     """
 }
nfcore-build/solutions/core-hello-part1/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..177)) ? 'retry' : 'finish' }
-    maxRetries    = 1
-    maxErrors     = '-1'
+    maxRetries = 1
... (truncated)
nfcore-build/solutions/core-hello-part1/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 }]
 }
nfcore-build/solutions/core-hello-part1/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)
nfcore-build/solutions/core-hello-part1/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
nfcore-build/solutions/core-hello-part1/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)
nfcore-build/solutions/core-hello-part1/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()
nfcore-build/solutions/core-hello-part1/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}
     """
 }
nfcore-build/solutions/core-hello-part1/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)
nfcore-build/solutions/core-hello-part1/modules/local/sayHello.nf
View 
@@ -13,6 +13,6 @@ process sayHello {
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
     """
 }
nfcore-build/solutions/core-hello-part1/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)
nfcore-build/solutions/core-hello-part1/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)
nfcore-build/solutions/core-hello-part1/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)
nfcore-build/solutions/core-hello-part1/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)
nfcore-build/solutions/core-hello-part1/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)
nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
nfcore-build/solutions/core-hello-part1/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
nfcore-build/solutions/core-hello-part1/workflows/hello.nf(truncated)
nfcore-build/solutions/core-hello-part2/conf/base.config(truncated)
nfcore-build/solutions/core-hello-part2/conf/modules.config(truncated)
nfcore-build/solutions/core-hello-part2/conf/test.config(truncated)
nfcore-build/solutions/core-hello-part2/conf/test_full.config(truncated)
nfcore-build/solutions/core-hello-part2/main.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/local/collectGreetings.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/local/convertToUpper.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/local/cowpy.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/local/sayHello.nf(truncated)
nfcore-build/solutions/core-hello-part2/modules/nf-core/find/concatenate/main.nf(truncated)
nfcore-build/solutions/core-hello-part2/nextflow.config(truncated)
nfcore-build/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf(truncated)
nfcore-build/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/main.nf(truncated)
nfcore-build/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config(truncated)
nfcore-build/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf(truncated)
nfcore-build/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
nfcore-build/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
nfcore-build/solutions/core-hello-part2/workflows/hello.nf(truncated)
nfcore-build/solutions/core-hello-part3/conf/base.config(truncated)
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nfcore-build/solutions/core-hello-part3/conf/test.config(truncated)
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nfcore-build/solutions/core-hello-part3/modules/local/collectGreetings.nf(truncated)
nfcore-build/solutions/core-hello-part3/modules/local/convertToUpper.nf(truncated)
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nfcore-build/solutions/core-hello-part3/modules/local/cowpy/main.nf(truncated)
nfcore-build/solutions/core-hello-part3/modules/local/sayHello.nf(truncated)
nfcore-build/solutions/core-hello-part3/modules/nf-core/find/concatenate/main.nf(truncated)
nfcore-build/solutions/core-hello-part3/nextflow.config(truncated)
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nfcore-build/solutions/core-hello-part3/subworkflows/nf-core/utils_nextflow_pipeline/main.nf(truncated)
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nfcore-build/solutions/core-hello-start/workflows/hello.nf(truncated)

@pinin4fjords pinin4fjords mentioned this pull request Oct 5, 2026
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