Template update for nf-core/tools version 3.0.2

nf-core · Oct 17, 2024 · 2bfd1d7 · 2bfd1d7
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -79,8 +79,6 @@ 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`.
-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`.
 
 ### Default values
 

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -21,5 +21,6 @@ template:
   outdir: .
   skip_features:
     - fastqc
-  version: 1.0dev
+    - multiqc
+  version: 0.0.1dev
 update: null
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## v0.0.1dev - [date]
 
 Initial release of nf-core/tfactivity, created with the [nf-core](https://nf-co.re/) template.
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -10,10 +10,6 @@
 
 ## Pipeline tools
 
-- [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.
-
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

diff --git a/README.md b/README.md
@@ -31,8 +31,6 @@
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
-
 ## Usage
 
 > [!NOTE]

diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
@@ -26,28 +26,6 @@ Content-Disposition: inline; filename="nf-core-tfactivity_logo_light.png"
     join( '\n' ) %>
 
 <%
-if (mqcFile){
-def mqcFileObj = new File("$mqcFile")
-if (mqcFileObj.length() < mqcMaxSize){
-out << """
---nfcoremimeboundary
-Content-Type: text/html; name=\"multiqc_report\"
-Content-Transfer-Encoding: base64
-Content-ID: <mqcreport>
-Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
-
-${mqcFileObj.
-    bytes.
-    encodeBase64().
-    toString().
-    tokenize( '\n' )*.
-    toList()*.
-    collate( 76 )*.
-    collect { it.join() }.
-    flatten().
-    join( '\n' )}
-"""
-}}
 %>
 
 --nfcoremimeboundary--
diff --git a/conf/modules.config b/conf/modules.config
@@ -19,13 +19,5 @@ 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 }
-        ]
-    }
 
 }
diff --git a/docs/output.md b/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.
 
 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.
 
@@ -12,25 +12,8 @@ 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:
 
-- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
-### MultiQC
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `multiqc/`
-  - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-  - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-  - `multiqc_plots/`: directory containing static images from the report in various formats.
-
-</details>
-
-[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>.
-
 ### Pipeline information
 
 <details markdown="1">

diff --git a/docs/usage.md b/docs/usage.md
@@ -110,7 +110,7 @@ It is a good idea to specify a pipeline version when running the pipeline on you
 
 First, go to the [nf-core/tfactivity releases page](https://github.com/nf-core/tfactivity/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.
 
 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.
 

diff --git a/main.nf b/main.nf
@@ -53,8 +53,6 @@ workflow NFCORE_TFACTIVITY {
     TFACTIVITY (
         samplesheet
     )
-    emit:
-    multiqc_report = TFACTIVITY.out.multiqc_report // channel: /path/to/multiqc_report.html
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -93,7 +91,7 @@ workflow {
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
-        NFCORE_TFACTIVITY.out.multiqc_report
+
     )
 }
 

diff --git a/modules.json b/modules.json
@@ -4,13 +4,7 @@
     "repos": {
         "https://github.com/nf-core/modules.git": {
             "modules": {
-                "nf-core": {
-                    "multiqc": {
-                        "branch": "master",
-                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
-                        "installed_by": ["modules"]
-                    }
-                }
+                "nf-core": {}
             },
             "subworkflows": {
                 "nf-core": {

diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml