1 changed files with 4 additions and 4 deletions
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- 4
tasks/CNVkit.wdl
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| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | ||||
| -r ${sample}.reference.cnn/reference.cnn \ | -r ${sample}.reference.cnn/reference.cnn \ | ||||
| --output-dir ${sample}.sampleid.cns \ | |||||
| --output-dir ${sample}.cns \ | |||||
| -p $nt | -p $nt | ||||
| #ls ./ | |||||
| #/root/miniconda2/bin/cnvkit.py call ${sample}.sampleid.cns \ | |||||
| # -o ${sample}.sampleid.call.cns | |||||
| ls ./ | |||||
| /root/miniconda2/bin/cnvkit.py call ${sample}.cns/${sample}.cns \ | |||||
| -o ${sample}.call.cns | |||||
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