#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "Filter single sample sv vcf from paired read callers(Manta/Smoove)" inputs: abundance_percentage: type: double? bam: type: File deletion_depth: type: double? duplication_depth: type: double? output_vcf_name: type: string? reference: type: string snps_vcf: type: File? sv_paired_count: type: int? sv_split_count: type: int? sv_vcf: type: File vcf_source: type: - type: enum symbols: ["manta", "smoove"] outputs: filtered_vcf: type: File outputSource: filtered_vcf_index/indexed_vcf steps: read_support_filter: run: ../tools/filter_sv_vcf_read_support.cwl in: abundance_percentage: abundance_percentage input_vcf: sv_vcf paired_count: sv_paired_count split_count: sv_split_count vcf_source: vcf_source out: [filtered_sv_vcf] duphold_annotate: run: ../tools/duphold.cwl in: bam: bam reference: reference snps_vcf: snps_vcf sv_vcf: read_support_filter/filtered_sv_vcf out: [annotated_sv_vcf] depth_filter: run: ../tools/filter_sv_vcf_depth.cwl in: input_vcf: duphold_annotate/annotated_sv_vcf deletion_depth: deletion_depth duplication_depth: duplication_depth output_vcf_name: output_vcf_name vcf_source: default: "duphold" out: [filtered_sv_vcf] filtered_vcf_bgzip: run: ../tools/bgzip.cwl in: file: depth_filter/filtered_sv_vcf out: [bgzipped_file] filtered_vcf_index: run: ../tools/index_vcf.cwl in: vcf: filtered_vcf_bgzip/bgzipped_file out: [indexed_vcf]