diff --git a/software/qualimap/bamqc/main.nf b/software/qualimap/bamqc/main.nf index d54dc704..a1426d93 100644 --- a/software/qualimap/bamqc/main.nf +++ b/software/qualimap/bamqc/main.nf @@ -31,10 +31,8 @@ process QUALIMAP_BAMQC { def software = getSoftwareName(task.process) prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" - def threads = task.cpus def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs' def memory = task.memory.toGiga() + "G" - def regions = use_gff ? "--gff $gff" : '' def strandedness = 'non-strand-specific' @@ -56,7 +54,7 @@ process QUALIMAP_BAMQC { -p $strandedness \\ $collect_pairs \\ -outdir $prefix \\ - -nt $threads + -nt $task.cpus echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//' > ${software}.version.txt """