subworkflows_merge_svs.cwl

Documentation for merge_svs.cwl

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Overview

Merge, annotate, and generate a TSV for SVs

Inputs

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?

Outputs

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

Steps

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