subworkflows_varscan_pre_and_post_processing.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'] | ||
| tumor_bam | File | ['^.bai', '.bai'] | ||
| normal_bam | File | ['^.bai'] | ||
| interval_list | File | |||
| strand_filter | int? | |||
| min_coverage | int? | |||
| min_var_freq | float? | |||
| p_value | float? | |||
| max_normal_freq | float? | |||
| normal_sample_name | string | |||
| tumor_sample_name | string | |||
| scatter_count | int |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| unfiltered_vcf | File | ['.tbi'] | ||
| filtered_vcf | File | ['.tbi'] |
| Name | CWL Run |
|---|---|
| split_interval_list | tools/split_interval_list.cwl |
| intervals_to_bed | tools/intervals_to_bed.cwl |
| varscan | subworkflows/varscan.cwl |
| merge_scattered_somatic_snvs | tools/picard_merge_vcfs.cwl |
| merge_scattered_somatic_indels | tools/picard_merge_vcfs.cwl |
| merge_scattered_somatic_hc_snvs | tools/picard_merge_vcfs.cwl |
| merge_scattered_somatic_hc_indels | tools/picard_merge_vcfs.cwl |
| merge_snvs | tools/set_filter_status.cwl |
| index_merged_snvs | tools/index_vcf.cwl |
| merge_indels | tools/set_filter_status.cwl |
| index_merged_indels | tools/index_vcf.cwl |
| merge | tools/merge_vcf.cwl |
| rename_tumor_sample | tools/replace_vcf_sample_name.cwl |
| rename_normal_sample | tools/replace_vcf_sample_name.cwl |
| index | tools/index_vcf.cwl |
| filter | subworkflows/fp_filter.cwl |