1 changed files with 2 additions and 1 deletions
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tasks/qualimap.wdl
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| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| /opt/qualimap/qualimap bamqc -bam ${bam} -gff ${regions} -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G | |||||
| 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} | tar -zcvf ${bamname}_qualimap.zip ${bamname} | ||||
| >>> | >>> | ||||
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