Fix multiple workflow in subworkflow

CHANGELOG.md

@@ -8,6 +8,7 @@
 - Add nf-core template version badges to README ([#3396](https://github.com/nf-core/tools/pull/3396))
 - Add Bluesky badge to readme ([#3475](https://github.com/nf-core/tools/pull/3475))
 - Run awsfulltest after release, and with dev revision on PRs to master ([#3485](https://github.com/nf-core/tools/pull/3485))
+- Separate `PIPELINE_COMPLETION` in its own file ([#3486](https://github.com/nf-core/tools/pull/3486))
 
 ### Linting
 
@@ -16,33 +17,37 @@
 - Fix: linting with comments after the input directive ([#3458](https://github.com/nf-core/tools/pull/3458))
 - EDAM ontology fixes ([#3460](https://github.com/nf-core/tools/pull/3460))
 - Fix default linting of nf-core components when `nf-core pipelines lint` is ran ([#3480](https://github.com/nf-core/tools/pull/3480))
+- Fix components linting in `nf-core subworkflows lint` with multiple workflows in a `main.nf` ([#3486](https://github.com/nf-core/tools/pull/3486))
 
 ### Modules
 
-- increase meta index for multiple input channels ([#3463](https://github.com/nf-core/tools/pull/3463))
+- Increase meta index for multiple input channels ([#3463](https://github.com/nf-core/tools/pull/3463))
 - Configure the default module repository, branch, and path from environment variables. ([#3481](https://github.com/nf-core/tools/pull/3481))
 
 ### Subworkflows
 
+- Forbid more than one `workflow` block by `main.nf` ([#3486](https://github.com/nf-core/tools/pull/3486))
+
 ### General
 
-- output passed to write_params_file as Path object ([#3435](https://github.com/nf-core/tools/pull/3435))
-- chore(deps): update python:3.12-slim docker digest to 69ce3ae ([#3433](https://github.com/nf-core/tools/pull/3433))
-- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.4 ([#3438](https://github.com/nf-core/tools/pull/3438))
-- format name/value with YAML syntax ([#3442](https://github.com/nf-core/tools/pull/3442))
-- chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.2.0 ([#3446](https://github.com/nf-core/tools/pull/3446))
-- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.5 ([#3445](https://github.com/nf-core/tools/pull/3445))
-- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.15.0 ([#3447](https://github.com/nf-core/tools/pull/3447))
+- Output passed to write_params_file as Path object ([#3435](https://github.com/nf-core/tools/pull/3435))
+- Chore(deps): update python:3.12-slim docker digest to 69ce3ae ([#3433](https://github.com/nf-core/tools/pull/3433))
+- Chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.4 ([#3438](https://github.com/nf-core/tools/pull/3438))
+- Format name/value with YAML syntax ([#3442](https://github.com/nf-core/tools/pull/3442))
+- Chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.2.0 ([#3446](https://github.com/nf-core/tools/pull/3446))
+- Chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.5 ([#3445](https://github.com/nf-core/tools/pull/3445))
+- Chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.15.0 ([#3447](https://github.com/nf-core/tools/pull/3447))
 - Update prettier to 3.5.0 ([#3448](https://github.com/nf-core/tools/pull/3448))
-- chore(deps): update python:3.12-slim docker digest to 34656cd ([#3450](https://github.com/nf-core/tools/pull/3450))
+- Chore(deps): update python:3.12-slim docker digest to 34656cd ([#3450](https://github.com/nf-core/tools/pull/3450))
 - Remove Twitter from README ([#3454](https://github.com/nf-core/tools/pull/3454))
-- docs: fix contributing link in the main README ([#3459](https://github.com/nf-core/tools/pull/3459))
+- Docs: fix contributing link in the main README ([#3459](https://github.com/nf-core/tools/pull/3459))
 - Cleanup: Removed Redundant if Condition ([#3468](https://github.com/nf-core/tools/pull/3468))
-- chore(deps): update gitpod/workspace-base docker digest to 7f35e40 ([#3473](https://github.com/nf-core/tools/pull/3473))
-- chore(deps): update python:3.12-slim docker digest to aaa3f8c ([#3474](https://github.com/nf-core/tools/pull/3474))
-- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.9 ([#3470](https://github.com/nf-core/tools/pull/3470))
-- chore(deps): update github actions ([#3488](https://github.com/nf-core/tools/pull/3488))
-- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.0 ([#3492](https://github.com/nf-core/tools/pull/3492))
+- Chore(deps): update gitpod/workspace-base docker digest to 7f35e40 ([#3473](https://github.com/nf-core/tools/pull/3473))
+- Chore(deps): update python:3.12-slim docker digest to aaa3f8c ([#3474](https://github.com/nf-core/tools/pull/3474))
+- Chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.9 ([#3470](https://github.com/nf-core/tools/pull/3470))
+- Chore(deps): update github actions ([#3488](https://github.com/nf-core/tools/pull/3488))
+- Chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.0 ([#3492](https://github.com/nf-core/tools/pull/3492))
+- Remove duplicated `pdiff` in `requirements.txt` ([#3486](https://github.com/nf-core/tools/pull/3486))
 
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
 

nf_core/pipeline-template/main.nf

@@ -20,7 +20,7 @@
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
 {%- if modules %}
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_pipeline_completion'
 {%- if igenomes %}
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_completion/main.nf

@@ -0,0 +1,86 @@
+//
+// Subworkflow with for pipeline completion
+//
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+{% if nf_schema %}
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+{% endif %}
+{%- if email %}
+include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+{%- endif %}
+include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
+{%- if adaptivecard or slackreport %}
+include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
+{%- endif %}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    SUBWORKFLOW FOR PIPELINE COMPLETION
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+workflow PIPELINE_COMPLETION {
+
+    take:
+    {%- if email %}
+    email           //  string: email address
+    email_on_fail   //  string: email address sent on pipeline failure
+    plaintext_email // boolean: Send plain-text email instead of HTML
+    {%- endif %}
+    outdir          //    path: Path to output directory where results will be published
+    monochrome_logs // boolean: Disable ANSI colour codes in log output
+    {%- if adaptivecard or slackreport %}
+    hook_url        //  string: hook URL for notifications
+    {% endif %}
+    {%- if multiqc %}
+    multiqc_report  //  string: Path to MultiQC report
+    {% endif %}
+
+    main:
+    {%- if nf_schema %}
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    {%- else %}
+    summary_params = [:]
+    {%- endif %}
+
+    {%- if multiqc %}
+    def multiqc_reports = multiqc_report.toList()
+    {%- endif %}
+
+    //
+    // Completion email and summary
+    //
+    workflow.onComplete {
+        {%- if email %}
+        if (email || email_on_fail) {
+            completionEmail(
+                summary_params,
+                email,
+                email_on_fail,
+                plaintext_email,
+                outdir,
+                monochrome_logs,
+                {% if multiqc %}multiqc_reports.getVal(),{% else %}[]{% endif %}
+            )
+        }
+        {%- endif %}
+
+        completionSummary(monochrome_logs)
+
+        {%- if adaptivecard or slackreport %}
+        if (hook_url) {
+            imNotification(summary_params, hook_url)
+        }
+        {%- endif %}
+    }
+
+    workflow.onError {
+        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+    }
+}

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_completion/meta.yml

@@ -0,0 +1,39 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "pipeline_completion"
+description: Notify user of pipeline completion
+keywords:
+  - notification
+  - email
+  - completion
+components: []
+input:
+  - email:
+      type: string
+      description: Email address
+  - email_on_fail:
+      type: string
+      description: Email address sent on pipeline failure
+  - plaintext_email:
+      type: boolean
+      description: Send plain-text email instead of HTML
+  - outdir:
+      type: string
+      description: Path to output directory where results will be published
+  - monochrome_logs:
+      type: boolean
+      description: Disable ANSI colour codes in log output
+  - hook_url:
+      type: string
+      description: Hook URL for notifications
+  - multiqc_report:
+      type: string
+      description: Path to MultiQC report
+output:
+  - dummy_emit:
+      type: boolean
+      description: |
+        Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@mirpedrol"
+maintainers:
+  - "@mirpedrol"

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -9,15 +9,7 @@
 */
 
 {% if nf_schema %}include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { samplesheetToList         } from 'plugin/nf-schema'{% endif %}
-{%- if email %}
-include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
-{%- endif %}
-include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-{%- if adaptivecard or slackreport %}
-include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
-{%- endif %}
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
@@ -112,70 +104,6 @@ workflow PIPELINE_INITIALISATION {
     versions    = ch_versions
 }
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    SUBWORKFLOW FOR PIPELINE COMPLETION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow PIPELINE_COMPLETION {
-
-    take:
-    {%- if email %}
-    email           //  string: email address
-    email_on_fail   //  string: email address sent on pipeline failure
-    plaintext_email // boolean: Send plain-text email instead of HTML
-    {%- endif %}
-    outdir          //    path: Path to output directory where results will be published
-    monochrome_logs // boolean: Disable ANSI colour codes in log output
-    {%- if adaptivecard or slackreport %}
-    hook_url        //  string: hook URL for notifications{% endif %}
-    {%- if multiqc %}
-    multiqc_report  //  string: Path to MultiQC report{% endif %}
-
-    main:
-    {%- if nf_schema %}
-    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    {%- else %}
-    summary_params = [:]
-    {%- endif %}
-
-    {%- if multiqc %}
-    def multiqc_reports = multiqc_report.toList()
-    {%- endif %}
-
-    //
-    // Completion email and summary
-    //
-    workflow.onComplete {
-        {%- if email %}
-        if (email || email_on_fail) {
-            completionEmail(
-                summary_params,
-                email,
-                email_on_fail,
-                plaintext_email,
-                outdir,
-                monochrome_logs,
-                {% if multiqc %}multiqc_reports.getVal(),{% else %}[]{% endif %}
-            )
-        }
-        {%- endif %}
-
-        completionSummary(monochrome_logs)
-
-        {%- if adaptivecard or slackreport %}
-        if (hook_url) {
-            imNotification(summary_params, hook_url)
-        }
-        {%- endif %}
-    }
-
-    workflow.onError {
-        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
-    }
-}
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/meta.yml

@@ -0,0 +1,48 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "pipeline_initialisation"
+description: Initialise the pipeline parameters, validate them and prepare the samplesheet
+keywords:
+  - initialisation
+  - validation
+  - parameters
+components: []
+input:
+  - version:
+      type: boolean
+      description: Display version and exit
+  - validate_params:
+      type: boolean
+      description: Boolean whether to validate parameters against the schema at runtime
+  - monochrome_logs:
+      type: boolean
+      description: Do not use coloured log outputs
+  - nextflow_cli_args:
+      type: array
+      description: List of positional nextflow CLI args
+  - outdir:
+      type: string
+      description: The output directory where the results will be saved
+  - input:
+      type: string
+      description: Path to input samplesheet
+output:
+  - samplesheet:
+      description: Channel with the samplesheet
+      structure:
+        - meta:
+          type: map
+          description: Metadata map
+        - fastq:
+          type: File
+          description: Fastq file
+          pattern: "*.fastq"
+  - versions:
+      description: Channel containing software versions file
+      structure:
+        - versions.yml:
+            type: file
+            description: File containing versions of the software used
+authors:
+  - "@mirpedrol"
+maintainers:
+  - "@mirpedrol"

nf_core/pipelines/create/create.py

@@ -314,6 +314,7 @@ def render_template(self) -> None:
         rename_files: Dict[str, str] = {
             "workflows/pipeline.nf": f"workflows/{short_name}.nf",
             "subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf": f"subworkflows/local/utils_nfcore_{short_name}_pipeline/main.nf",
+            "subworkflows/local/utils_nfcore_pipeline_pipeline/meta.yml": f"subworkflows/local/utils_nfcore_{short_name}_pipeline/meta.yml",
         }
 
         # Set the paths to skip according to customization