template: workflow output for multiQC

.github/workflows/create-lint-wf.yml

@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "25.04.0"
+          - "25.10.0"
           - "latest-everything"
     steps:
       - name: go to subdirectory and change nextflow workdir

.github/workflows/create-test-wf.yml

@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "25.04.0"
+          - "25.10.0"
           - "latest-everything"
     steps:
       - name: go to working directory

nf_core/pipeline-template/.github/workflows/nf-test.yml

@@ -80,7 +80,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.10.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

nf_core/pipeline-template/README.md

@@ -21,7 +21,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-{{ nf_core_version }}-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/{{ nf_core_version }})
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

nf_core/pipeline-template/conf/modules.config

@@ -29,11 +29,6 @@ process {
 
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-        publishDir = [
-            path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
     {%- endif %}
 

nf_core/pipeline-template/main.nf

@@ -66,6 +66,8 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
 {%- if multiqc %}{%- if modules %}
     emit:
     multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
+    multiqc_data   = {{ short_name|upper }}.out.multiqc_data // channel: [meta, /path/to/multiqc_data/]
+    multiqc_plots  = {{ short_name|upper }}.out.multiqc_plots // channel: [meta, /path/to/multiqc_plots/]
 {%- endif %}{%- endif %}
 }
 /*
@@ -122,6 +124,22 @@ workflow {
         {{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
     )
     {%- endif %}
+{%- if multiqc %}{%- if modules %}
+
+    def multiqc_publish = {{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report
+        .mix({{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_data)
+        .mix({{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_plots)
+
+    publish:
+    multiqc = multiqc_publish
+}
+
+output {
+    multiqc {
+        path "multiqc"
+    }
+{%- endif %}{%- endif %}
+
 }
 
 /*

nf_core/pipeline-template/nextflow.config

@@ -70,6 +70,12 @@ params {
     {%- endif %}
 }
 
+// Backwards compatibility for publishDir syntax
+outputDir = params.outdir
+{%- if modules %}
+workflow.output.mode = params.publish_dir_mode
+{%- endif %}
+
 {% if modules -%}
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -306,7 +312,7 @@ manifest {
     description     = """{{ description }}"""
     mainScript      = 'main.nf'
     defaultBranch   = '{{ default_branch }}'
-    nextflowVersion = '!>=25.04.0'
+    nextflowVersion = '!>=25.10.0'
     version         = '{{ version }}'
     doi             = ''
 }

nf_core/pipeline-template/tests/default.nf.test

@@ -5,6 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
 
     test("-profile test") {
+        options "-output-dir $outputDir"
 
         when {
             params {

nf_core/pipeline-template/workflows/pipeline.nf

@@ -115,7 +115,9 @@ workflow {{ short_name|upper }} {
     )
 {% endif %}
     emit:
-    {%- if multiqc %}multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html{% endif %}
+    {%- if multiqc %}multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html
+    multiqc_data   = MULTIQC.out.data // channel: [meta, /path/to/multiqc_data/]
+    multiqc_plots  = MULTIQC.out.plots // channel: [meta, /path/to/multiqc_plots/]{% endif %}
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
 {%- else %}
 

nf_core/pipelines/lint/readme.py

@@ -53,7 +53,7 @@ def readme(self):
 
     if "nextflow_badge" not in ignore_configs:
         # Check that there is a readme badge showing the minimum required version of Nextflow
-        # [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+        # [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
         # and that it has the correct version
         nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/version-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-green\?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow\.io\)\]\(https://www\.nextflow\.io/\)"
         match = re.search(nf_badge_re, content)