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revise qualimap

tags/v0.1.0
stead99 4 年之前
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a7b69feda7
共有 1 個檔案被更改,包括 4 行新增4 行删除
  1. +4
    -4
      tasks/qualimap.wdl

+ 4
- 4
tasks/qualimap.wdl 查看文件

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 /opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=10G
tar -zcvf ${bamname}_rnaseq_qualimap.zip ${bamname}_rnaseq
/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G /opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G
tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc
tar -zcf ${bamname}_rnaseq_qualimap.tar.gz ${bamname}_rnaseq
tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc
>>> >>>


runtime { runtime {
} }


output { output {
File rnaseq_zip = "${bamname}_rnaseq_qualimap.zip"
File bamqc_zip = "${bamname}_bamqc_qualimap.zip"
File rnaseq_gz = "${bamname}_rnaseq_qualimap.tar.gz"
File bamqc_gz = "${bamname}_bamqc_qualimap.tar.gz"
} }
} }

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