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tasks/batch.wdl
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| cd /cromwell_root/tmp/cnvkit | cd /cromwell_root/tmp/cnvkit | ||||
| mkdir results | mkdir results | ||||
| cnvkit.py batch -p $nt ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \ | cnvkit.py batch -p $nt ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \ | ||||
| --method ${method} --segment-method ${segment_method} \ | |||||
| --method ${method} \ | |||||
| ${access_opt} ${annotate_opt} \ | ${access_opt} ${annotate_opt} \ | ||||
| --fasta hg_ref.fa ${reference_opt} \ | --fasta hg_ref.fa ${reference_opt} \ | ||||
| --output-reference ${sample_id}.reference.cnn \ | --output-reference ${sample_id}.reference.cnn \ |
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