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tasks/CNVkit.wdl
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| String? Ploidy | String? Ploidy | ||||
| File tumor_bam | File tumor_bam | ||||
| File tumor_bam_index | File tumor_bam_index | ||||
| Array[File]? normal_bams | |||||
| Array[File]? normal_bam_indexs | |||||
| File? normal_bam | File? normal_bam | ||||
| File? normal_bam_index | File? normal_bam_index | ||||
| String docker | String docker | ||||
| echo $center | echo $center | ||||
| if [ ${sep=" " normal_bams} ];then | |||||
| echo ${sep=" " normal_bams} | |||||
| /usr/local/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed | |||||
| /usr/local/bin/cnvkit.py batch ${tumor_bam} \ | |||||
| --normal ${sep=" " normal_bams} \ | |||||
| --targets my_baits.bed \ | |||||
| --fasta ${ref_dir} \ | |||||
| --annotate ${ref_flat} -p $nt \ | |||||
| --drop-low-coverage \ | |||||
| --output-dir ${sample}.reference.cnn | |||||
| #WES | #WES | ||||
| if [ ${bed_file} ]; then | if [ ${bed_file} ]; then | ||||
| echo "WES" | echo "WES" |
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