1 changed files with 4 additions and 4 deletions
+ 4
- 4
tasks/CNVkit.wdl
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| --fasta ${ref_dir} \ | --fasta ${ref_dir} \ | ||||
| --annotate ${ref_flat} -p $nt \ | --annotate ${ref_flat} -p $nt \ | ||||
| --drop-low-coverage \ | --drop-low-coverage \ | ||||
| --output-dir ${sample}.reference.cnn | |||||
| --output-dir ${sample_id}.reference.cnn | |||||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \ | ||||
| -r ${sample}.reference.cnn \ | |||||
| --output-dir ${sample}.sampleid.cns \ | |||||
| -r ${sample_id}.reference.cnn \ | |||||
| --output-dir ${sample_id}.sampleid.cns \ | |||||
| -p $nt | -p $nt | ||||
| /root/miniconda2/bin/cnvkit.py call ${sample}.sampleid.cns \ | /root/miniconda2/bin/cnvkit.py call ${sample}.sampleid.cns \ | ||||
| -o ${sample}.sampleid.call.cns | |||||
| -o ${sample_id}.sampleid.call.cns | |||||
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