1 changed files with 7 additions and 2 deletions
+ 7
- 2
tasks/CNVkit.wdl
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| File tumor_bam_index | File tumor_bam_index | ||||
| File? normal_bam | File? normal_bam | ||||
| File? normal_bam_index | File? normal_bam_index | ||||
| File? VCF | |||||
| String docker | String docker | ||||
| String cluster_config | String cluster_config | ||||
| String disk_size | String disk_size | ||||
| -p $nt | -p $nt | ||||
| ls ./ | ls ./ | ||||
| /usr/local/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \ | |||||
| -o ${sample}.call.cns | |||||
| if [ ${VCF} ]; then | |||||
| /usr/local/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \ | |||||
| -o ${sample}.call.cns | |||||
| else | |||||
| /usr/local/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center --vcf ${VCF}\ | |||||
| -o ${sample}.call.cns | |||||
| # Plot the results | # Plot the results |
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