1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/CNVkit.wdl
View File
| @@ -2,7 +2,7 @@ | |||
| task cnvkit{ | |||
| String sample | |||
| File ref_dir | |||
| String fasta | |||
| String? fasta | |||
| File ref_flat | |||
| File tumor_bam | |||
| File tumor_bam_index | |||
| @@ -17,7 +17,7 @@ task cnvkit{ | |||
| set -o pipefail | |||
| set -e | |||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir}/${fasta} --annotate ${ref_flat} | |||
| /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} | |||
| /root/miniconda2/bin/cnvkit.py scatter ${sample}.cnr -s ${sample}.cns -o ${sample}_scatter.pdf | |||
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