1 changed files with 5 additions and 1 deletions
+ 5
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tasks/CNVkit.wdl
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| nt=$(nproc) | nt=$(nproc) | ||||
| echo ${sample} | echo ${sample} | ||||
| center=`awk -v vv=${center_at} 'BEGIN {print log(2/vv)/log(2)}'` | |||||
| echo $center | |||||
| if [ ${normal_bam} ]; then | if [ ${normal_bam} ]; then | ||||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | ||||
| -p $nt | -p $nt | ||||
| ls ./ | ls ./ | ||||
| /root/miniconda2/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at ${center_at} \ | |||||
| /root/miniconda2/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \ | |||||
| -o ${sample}.call.cns | -o ${sample}.call.cns | ||||
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