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subworkflows_varscan_germline.cwl
Travis CI User edited this page Feb 24, 2021
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Varscan Workflow
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| reference | ['string', 'File'] | ['.fai', '^.dict'] | ||
| bam | File | ['.bai', '^.bai'] | ||
| interval_list | File | |||
| strand_filter | int? | |||
| min_coverage | int? | |||
| min_var_freq | float? | |||
| min_reads | int? | |||
| p_value | float? | |||
| max_normal_freq | float? | |||
| sample_name | string |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| unfiltered_vcf | File | ['.tbi'] | ||
| filtered_vcf | File | ['.tbi'] |
| Name | CWL Run |
|---|---|
| intervals_to_bed | tools/intervals_to_bed.cwl |
| varscan | tools/varscan_germline.cwl |
| bgzip_and_index | subworkflows/bgzip_and_index.cwl |
| filter | subworkflows/fp_filter.cwl |