Update subworkflows/nf-core/qc_markduplicates.nf

maxulysse · FriederikeHanssen · web-flow · commit 4d55e71e5797 · 2021-08-04T14:32:36.000+02:00
Co-authored-by: FriederikeHanssen &lt;Friederike.hanssen@qbic.uni-tuebingen.de&gt;
diff --git a/subworkflows/nf-core/qc_markduplicates.nf b/subworkflows/nf-core/qc_markduplicates.nf
@@ -80,6 +80,7 @@ workflow QC_MARKDUPLICATES {
     //After bamqc finishes, convert to cram for further analysis
     qualimap_bamqc = Channel.empty()
     if (!skip_bamqc && !skip_markduplicates) {
+    //TODO: after adding CI tests, allow bamqc on mapped bams if no duplicate marking is done
         QUALIMAP_BAMQC(bam_markduplicates, target_bed, params.target_bed)
         qualimap_bamqc = QUALIMAP_BAMQC.out
     }

Original file line number	Diff line number	Diff line change
`@@ -80,6 +80,7 @@ workflow QC_MARKDUPLICATES {`
`80`	`80`	`//After bamqc finishes, convert to cram for further analysis`
`81`	`81`	`qualimap_bamqc = Channel.empty()`
`82`	`82`	`if (!skip_bamqc && !skip_markduplicates) {`
	`83`	`+ //TODO: after adding CI tests, allow bamqc on mapped bams if no duplicate marking is done`
`83`	`84`	`QUALIMAP_BAMQC(bam_markduplicates, target_bed, params.target_bed)`
`84`	`85`	`qualimap_bamqc = QUALIMAP_BAMQC.out`
`85`	`86`	`}`