Template update for nf-core/tools version 3.0.2

nf-core · Oct 16, 2024 · 60b0df5 · 60b0df5
1 parent f6286bc
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Showing 14 changed files with 6 additions and 877 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -19,6 +19,7 @@ template:
   name: tfactivity
   org: nf-core
   outdir: .
-  skip_features: null
+  skip_features:
+    - fastqc
   version: 1.0dev
 update: null
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -10,10 +10,6 @@
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
-
 - [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.

diff --git a/README.md b/README.md
@@ -31,7 +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 -->
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage

diff --git a/conf/modules.config b/conf/modules.config
@@ -18,9 +18,7 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: FASTQC {
-        ext.args = '--quiet'
-    }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

diff --git a/docs/output.md b/docs/output.md
@@ -12,23 +12,9 @@ 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
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
-### FastQC
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `fastqc/`
-  - `*_fastqc.html`: FastQC report containing quality metrics.
-  - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
-
-</details>
-
-[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
 
 <details markdown="1">

diff --git a/modules.json b/modules.json
@@ -5,11 +5,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "fastqc": {
-                        "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
-                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",

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