Merge pull request #186 from apeltzer/fastqc-optional

Add Skipping FastQC

Author: apeltzer

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)
 

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. 

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