1 changed files with 3 additions and 1 deletions
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tasks/CNVkit.wdl
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| String docker | String docker | ||||
| String cluster_config | String cluster_config | ||||
| String disk_size | String disk_size | ||||
| String sample=basename(sample_id,".bam") | |||||
| String sample=basename(tumor_bam,".bam") | |||||
| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| echo ${sample} | |||||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} --diagram --scatter | /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} --diagram --scatter | ||||
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