1 changed files with 2 additions and 1 deletions
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tasks/CNVkit.wdl
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| File ref_dir | File ref_dir | ||||
| String? fasta | String? fasta | ||||
| File ref_flat | File ref_flat | ||||
| File bed_file | |||||
| File tumor_bam | File tumor_bam | ||||
| File tumor_bam_index | File tumor_bam_index | ||||
| File? normal_bam | File? normal_bam | ||||
| --method wgs \ | --method wgs \ | ||||
| --fasta ${ref_dir} \ | --fasta ${ref_dir} \ | ||||
| --annotate ${ref_flat} -p $nt \ | --annotate ${ref_flat} -p $nt \ | ||||
| --targets targets.bed \ | |||||
| --targets ${bed_file} \ | |||||
| --drop-low-coverage \ | --drop-low-coverage \ | ||||
| --output-dir ${sample_id}.reference.cnn | --output-dir ${sample_id}.reference.cnn | ||||
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