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tasks/qualimap.wdl
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| @@ -11,7 +11,7 @@ task qualimap { | |||
| set -e | |||
| nt=$(nproc) | |||
| /opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G | |||
| /opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe -s --java-mem-size=32G | |||
| /opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=32G | |||
| tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc | |||
| tar -zcf ${bamname}_rnaseq_qualimap.tar.gz ${bamname}_rnaseq | |||
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