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tasks/qualimap.wdl
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| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| /opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G | /opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G | ||||
| /opt/qualimap/qualimap rnaseq -bam ${bam_percent} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=32G | |||||
| tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc | tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc | ||||
| tar -zcf ${bamname}_rnaseq_qualimap.tar.gz ${bamname}_rnaseq | |||||
| >>> | >>> | ||||
| output { | output { | ||||
| File bamqc_gz="${bamname}_bamqc_qualimap.tar.gz" | File bamqc_gz="${bamname}_bamqc_qualimap.tar.gz" | ||||
| File rnaseq_gz="${bamname}_rnaseq_qualimap.tar.gz" | |||||
| } | } | ||||
| } | } |
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