diff --git a/CHANGELOG.md b/CHANGELOG.md index 72189363c..8ff9a17af 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Added` +* [#186](https://github.com/nf-core/eager/pull/186) - Make FastQC skipping [possible] +/(https://github.com/nf-core/eager/issues/182) ### `Fixed` * [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171) diff --git a/docs/usage.md b/docs/usage.md index 05bdb36bb..436f92e9e 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -299,6 +299,10 @@ Turns off the computation of library complexity estimation. Turns off adaptor trimming and paired-end read merging. Equivalent to setting both `--skip_collapse` and `--skip_trim`. +### `--skip_fastqc` + +Turns off FastQC in the beginning to speed up the pipeline. + ### `--skip_damage_calculation` Turns off the DamageProfiler module to compute DNA damage profiles. diff --git a/main.nf b/main.nf index 5b807c8ef..22470deff 100644 --- a/main.nf +++ b/main.nf @@ -148,6 +148,7 @@ params.email = false params.plaintext_email = false // Skipping parts of the pipeline for impatient users +params.skip_fastqc = false params.skip_adapterremoval = false params.skip_preseq = false params.skip_damage_calculation = false @@ -532,6 +533,8 @@ process fastqc { publishDir "${params.outdir}/FastQC", mode: 'copy', saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"} + when: !params.skip_fastqc + input: set val(name), file(reads) from ch_read_files_fastqc.mix(ch_read_files_converted_fastqc) @@ -650,7 +653,7 @@ process fastqc_after_clipping { publishDir "${params.outdir}/FastQC/after_clipping", mode: 'copy', saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"} - when: !params.bam && !params.skip_adapterremoval + when: !params.bam && !params.skip_adapterremoval && !params.skip_fastqc input: set val(name), file(reads) from ch_clipped_reads_for_fastqc