subworkflows_docm_germline.cwl
APipe Tester edited this page Apr 27, 2022
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Detect DoCM variants
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| reference | ['string', 'File'] | ['.fai', '^.dict'] | ||
| bam | File | ['^.bai'] | ||
| docm_vcf | File | ['.tbi'] | ||
| interval_list | File |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| unfiltered_vcf | File | |||
| filtered_vcf | File | ['.tbi'] |
| Name | CWL Run |
|---|---|
| gatk_haplotypecaller | tools/docm_gatk_haplotype_caller.cwl |
| bgzip | tools/bgzip.cwl |
| index | tools/index_vcf.cwl |
| decompose | tools/vt_decompose.cwl |
| docm_filter | tools/single_sample_docm_filter.cwl |
| bgzip2 | tools/bgzip.cwl |
| index2 | tools/index_vcf.cwl |