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subworkflows_bam_readcount.cwl
Travis CI User edited this page Dec 9, 2019
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bam_readcount workflow
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| vcf | File | ['.tbi'] | ||
| sample | string | |||
| reference_fasta | ['string', 'File'] | ['.fai', '^.dict'] | ||
| bam | File | ['.bai'] | ||
| min_base_quality | int? | |||
| min_mapping_quality | int? |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| normalized_vcf | File | |||
| snv_bam_readcount_tsv | File | |||
| indel_bam_readcount_tsv | File |
| Name | CWL Run |
|---|---|
| normalize_variants | tools/normalize_variants.cwl |
| decompose_variants | tools/vt_decompose.cwl |
| bam_readcount | tools/bam_readcount.cwl |