1 changed files with 4 additions and 2 deletions
+ 4
- 2
tasks/CNVkit.wdl
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| String? fasta | String? fasta | ||||
| File ref_flat | File ref_flat | ||||
| File bed_file | File bed_file | ||||
| String center_at | |||||
| File hrd | |||||
| File tumor_bam | File tumor_bam | ||||
| File tumor_bam_index | File tumor_bam_index | ||||
| File? normal_bam | File? normal_bam | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| echo ${sample} | echo ${sample} | ||||
| PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'` | |||||
| center=`awk -v vv=${center_at} 'BEGIN {print log(2/vv)/log(2)}'` | |||||
| center=`awk -v vv=$PURITY 'BEGIN {print log(2/vv)/log(2)}'` | |||||
| echo $center | echo $center | ||||
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