Zhihui
4 years ago
3 changed files with 6 additions and 6 deletions
BIN
.DS_Store
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+ 3
- 3
tasks/qualimapBAMqc.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} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G | |||||
| tar -zcvf ${bamname}.zip ${bamname}_bamqc | |||||
| /opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G | |||||
| tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname} | |||||
| >>> | >>> | ||||
| } | } | ||||
| output { | output { | ||||
| File bamqc_zip = "${bamname}.zip" | |||||
| File bamqc_zip = "${bamname}_bamqc_qualimap.zip" | |||||
| } | } | ||||
| } | } |
+ 3
- 3
tasks/qualimapRNAseq.wdl
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| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| /opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_RNAseq -gtf ${gtf} -pe --java-mem-size=10G | |||||
| tar -zcvf ${bamname}.zip ${bamname}_RNAseq | |||||
| /opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname} -gtf ${gtf} -pe --java-mem-size=10G | |||||
| tar -zcvf ${bamname}_RNAseq_qualimap.zip ${bamname} | |||||
| >>> | >>> | ||||
| } | } | ||||
| output { | output { | ||||
| File rnaseq_zip = "${bamname}.zip" | |||||
| File rnaseq_zip = "${bamname}_RNAseq_qualimap.zip" | |||||
| } | } | ||||
| } | } |
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