2 changed files with 3 additions and 2 deletions
BIN
.DS_Store
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+ 3
- 2
tasks/qualimapBAMqc.wdl
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| @@ -11,8 +11,9 @@ task qualimapBAMqc { | |||
| set -o pipefail | |||
| set -e | |||
| nt=$(nproc) | |||
| /opt/qualimap/qualimap bamqc -bam ${bam} -regions ${regions} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G | |||
| tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc | |||
| awk 'BEGIN{OFS="\t"}{sub("\r","",$3);print $1,$2,$3,"",0,"."}' ${regions} > new.bed | |||
| /opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G | |||
| tar -zcvf ${bamname}_qualimap.zip ${bamname} | |||
| >>> | |||
| runtime { | |||
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