Merge pull request #3103 from mirpedrol/template-customisation-mutiqc

Template: add option to exclude multiqc from pipeline template

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

@@ -44,6 +44,7 @@ jobs:
           - "template_skip_code_linters.yml"
           - "template_skip_citations.yml"
           - "template_skip_gitpod.yml"
+          - "template_skip_multiqc.yml"
         runner:
           # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
           - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
@@ -117,6 +118,10 @@ jobs:
         run: |
           printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml
 
+      - name: Create template skip multiqc
+        run: |
+          printf "org: my-prefix\nskip: multiqc" > create-test-lint-wf/template_skip_multiqc.yml
+
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |

.prettierignore

@@ -5,6 +5,8 @@ docs/api/_build
 testing
 nf_core/module-template/meta.yml
 nf_core/pipeline-template/nextflow_schema.json
+nf_core/pipeline-template/modules.json
+nf_core/pipeline-template/tower.yml
 # don't run on things handled by ruff
 *.py
 *.pyc

CHANGELOG.md

@@ -12,6 +12,7 @@
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
 - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101))
 - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
+- add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103))
 
 ### Linting
 

nf_core/pipeline-template/.github/CONTRIBUTING.md

@@ -87,8 +87,10 @@ If you wish to contribute a new step, please use the following coding standards:
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+   {%- if multiqc %}
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+    {% endif %}
 
 ### Default values
 

nf_core/pipeline-template/CITATIONS.md

@@ -16,9 +16,10 @@
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+> {%- endif %}
 
 ## Software packaging/containerisation tools
 

nf_core/pipeline-template/README.md

@@ -45,7 +45,7 @@
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+   {% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %}
 
 ## Usage
 

nf_core/pipeline-template/assets/sendmail_template.txt

@@ -26,6 +26,7 @@ Content-Disposition: inline; filename="{{ name_noslash }}_logo_light.png"
     join( '\n' ) %>
 
 <%
+{%- if multiqc %}
 if (mqcFile){
 def mqcFileObj = new File("$mqcFile")
 if (mqcFileObj.length() < mqcMaxSize){
@@ -48,6 +49,7 @@ ${mqcFileObj.
     join( '\n' )}
 """
 }}
+{%- endif %}
 %>
 
 --nfcoremimeboundary--

nf_core/pipeline-template/conf/modules.config

@@ -22,6 +22,7 @@ process {
         ext.args = '--quiet'
     }
 
+    {%- if multiqc %}
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
@@ -30,5 +31,6 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+    {%- endif %}
 
 }

nf_core/pipeline-template/docs/output.md

@@ -2,7 +2,7 @@
 
 ## Introduction
 
-This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
+This document describes the output produced by the pipeline. {% if multiqc %}Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.{% endif %}
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
@@ -13,7 +13,7 @@ The directories listed below will be created in the results directory after the
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [FastQC](#fastqc) - Raw read QC
-- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+  {% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %}
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQC
@@ -29,15 +29,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
-
-![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
-
-![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
-
-:::note
-The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-:::
+{%- if multiqc %}
 
 ### MultiQC
 
@@ -54,6 +46,7 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+{% endif %}
 
 ### Pipeline information
 

nf_core/pipeline-template/docs/usage.md

@@ -114,7 +114,7 @@ It is a good idea to specify a pipeline version when running the pipeline on you
 
 First, go to the [{{ name }} releases page](https://github.com/{{ name }}/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. {% if multiqc %}For example, at the bottom of the MultiQC reports.{% endif %}
 
 To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 

nf_core/pipeline-template/main.nf

@@ -56,10 +56,10 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
     {{ short_name|upper }} (
         samplesheet
     )
-
+{%- if multiqc %}
     emit:
     multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
-
+{%- endif %}
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -101,7 +101,7 @@ workflow {
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
-        {{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report
+        {%- if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
     )
 }
 

nf_core/pipeline-template/modules.json

@@ -9,12 +9,13 @@
                         "branch": "master",
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
-                    },
+                    }{%- if multiqc %},
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     }
+                    {%- endif %}
                 }
             },
             "subworkflows": {

nf_core/pipeline-template/nextflow.config

@@ -20,13 +20,14 @@ params {
     igenomes_ignore            = false
     {%- endif %}
 
+    {%- if multiqc %}
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
     multiqc_logo               = null
     max_multiqc_email_size     = '25.MB'
-    {%- if citations %}
-    multiqc_methods_description = null{% endif %}
+    {% if citations %}multiqc_methods_description = null{% endif %}
+    {%- endif %}
 
     // Boilerplate options
     outdir                       = null

nf_core/pipeline-template/nextflow_schema.json

@@ -35,12 +35,13 @@
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
-                },
+                }{% if multiqc %},
                 "multiqc_title": {
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
                 }
+                {% endif %}
             }
         },
         {%- if igenomes %}
@@ -201,6 +202,7 @@
                     "fa_icon": "fas fa-remove-format",
                     "hidden": true
                 },
+                {%- if multiqc %}
                 "max_multiqc_email_size": {
                     "type": "string",
                     "description": "File size limit when attaching MultiQC reports to summary emails.",
@@ -209,6 +211,7 @@
                     "fa_icon": "fas fa-file-upload",
                     "hidden": true
                 },
+                {% endif %}
                 "monochrome_logs": {
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",
@@ -222,6 +225,7 @@
                     "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
                 },
+                {%- if multiqc %}
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",
@@ -239,7 +243,7 @@
                     "type": "string",
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
-                },{% endif %}
+                },{% endif %}{% endif %}
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",

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

@@ -123,7 +123,7 @@ workflow PIPELINE_COMPLETION {
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
-    multiqc_report  //  string: Path to MultiQC report
+    {% if multiqc %}multiqc_report  //  string: Path to MultiQC report{% endif %}
 
     main:
 
@@ -134,7 +134,11 @@ workflow PIPELINE_COMPLETION {
     //
     workflow.onComplete {
         if (email || email_on_fail) {
+            {%- if multiqc %}
             completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+            {%- else %}
+            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, [])
+            {%- endif %}
         }
 
         completionSummary(monochrome_logs)
@@ -206,8 +210,7 @@ def genomeExistsError() {
     }
 }
 {%- endif %}
-
-{%- if citations %}
+{%- if citations or multiqc %}
 //
 // Generate methods description for MultiQC
 //

nf_core/pipeline-template/tower.yml

@@ -1,5 +1,7 @@
 reports:
+  {%- if multiqc %}
   multiqc_report.html:
     display: "MultiQC HTML report"
+  {%- endif %}
   samplesheet.csv:
     display: "Auto-created samplesheet with collated metadata and FASTQ paths"

nf_core/pipeline-template/workflows/pipeline.nf

@@ -5,11 +5,11 @@
 */
 
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                } from '../modules/nf-core/multiqc/main'
+{% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
 include { paramsSummaryMap       } from 'plugin/nf-validation'
-include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+{% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-{% if citations %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
+{% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -25,15 +25,15 @@ workflow {{ short_name|upper }} {
     main:
 
     ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
+    {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %}
 
     //
     // MODULE: Run FastQC
     //
     FASTQC (
         ch_samplesheet
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
+    {% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}){% endif %}
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     //
@@ -47,6 +47,7 @@ workflow {{ short_name|upper }} {
             newLine: true
         ).set { ch_collated_versions }
 
+{% if multiqc %}
     //
     // MODULE: MultiQC
     //
@@ -89,9 +90,9 @@ workflow {{ short_name|upper }} {
         ch_multiqc_custom_config.toList(),
         ch_multiqc_logo.toList()
     )
-
+{% endif %}
     emit:
-    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    {%- if multiqc %}multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html{% endif %}
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
 }