1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/stralka.wdl
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| String ref_fasta | String ref_fasta | ||||
| File ref_dir | File ref_dir | ||||
| String sample_id | String sample_id | ||||
| File ref_bed | |||||
| String ref_bed | |||||
| File? manta_indel_vcf | File? manta_indel_vcf | ||||
| File? manta_indel_vcf_index | File? manta_indel_vcf_index | ||||
| --normalBam ${normal_bam} \ | --normalBam ${normal_bam} \ | ||||
| --tumorBam ${tumor_bam} \ | --tumorBam ${tumor_bam} \ | ||||
| --referenceFasta ${ref_dir}/${ref_fasta} \ | --referenceFasta ${ref_dir}/${ref_fasta} \ | ||||
| --callRegions ${ref_bed} \ | |||||
| --callRegions ${ref_dir}/${ref_bed} \ | |||||
| --runDir ${out_dir} | --runDir ${out_dir} | ||||
| ls ${out_dir} | ls ${out_dir} |
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