subworkflows_merge_svs.cwl
Travis CI User edited this page Feb 24, 2021
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Merge, annotate, and generate a TSV for SVs
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| cohort_name | string? | |||
| estimate_sv_distance | boolean | |||
| genome_build | string | |||
| max_distance_to_merge | int | |||
| minimum_sv_calls | int | |||
| minimum_sv_size | int | |||
| same_strand | boolean | |||
| same_type | boolean | |||
| snps_vcf | File? | |||
| sv_vcfs | File[] | |||
| blocklist_bedpe | File? |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| bcftools_merged_sv_vcf | File | |||
| bcftools_merged_annotated_tsv | File | |||
| bcftools_merged_filtered_annotated_tsv | File | |||
| survivor_merged_sv_vcf | File | |||
| survivor_merged_annotated_tsv | File |
| Name | CWL Run |
|---|---|
| survivor_merge_sv_vcfs | tools/survivor.cwl |
| filter_blocklist_survivor | tools/filter_sv_vcf_blocklist_bedpe.cwl |
| survivor_annotate_variants | tools/annotsv.cwl |
| bcftools_merge_sv_vcfs | tools/bcftools_merge.cwl |
| filter_blocklist_bcftools | tools/filter_sv_vcf_blocklist_bedpe.cwl |
| bcftools_annotate_variants | tools/annotsv.cwl |
| bcftools_annotsv_filter | tools/annotsv_filter.cwl |