2 changed files with 2 additions and 3 deletions
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- 1
tasks/hisat2.wdl
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| } | } | ||||
| output { | output { | ||||
| File sam=sample_id + ".sam" | |||||
| File unmapread_1p=sample_id + "_un.fq.1.gz" | File unmapread_1p=sample_id + "_un.fq.1.gz" | ||||
| File unmapread_2p=sample_id + "_un.fq.2.gz" | File unmapread_2p=sample_id + "_un.fq.2.gz" | ||||
| } | } |
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- 2
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} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G | |||||
| tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc | |||||
| /opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname} --java-mem-size=32G | |||||
| tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname} | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
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