1 changed files with 2 additions and 1 deletions
+ 2
- 1
tasks/CNVkit.wdl
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| @@ -5,6 +5,7 @@ task cnvkit{ | |||
| String? fasta | |||
| File ref_flat | |||
| File bed_file | |||
| String center_at | |||
| File tumor_bam | |||
| File tumor_bam_index | |||
| File? normal_bam | |||
| @@ -48,7 +49,7 @@ task cnvkit{ | |||
| -p $nt | |||
| ls ./ | |||
| /root/miniconda2/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at -0.51 \ | |||
| /root/miniconda2/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at ${center_at} \ | |||
| -o ${sample}.call.cns | |||
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