#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "exome alignment and germline variant detection" requirements: - class: SubworkflowFeatureRequirement inputs: reference: type: string cram: type: File emit_reference_confidence: type: string gvcf_gq_bands: type: string[] intervals: type: type: array items: type: array items: string contamination_fraction: type: string? vep_cache_dir: type: string? synonyms_file: type: File? coding_only: type: boolean? hgvs_annotation: type: boolean? custom_gnomad_vcf: type: File? secondaryFiles: [.tbi] limit_variant_intervals: type: File outputs: gvcf: type: File[] outputSource: haplotype_caller/gvcf final_vcf: type: File outputSource: index_annotated_vcf/indexed_vcf secondaryFiles: [.tbi] coding_vcf: type: File outputSource: index_coding_vcf/indexed_vcf secondaryFiles: [.tbi] limited_vcf: type: File outputSource: limit_variants/filtered_vcf secondaryFiles: [.tbi] vep_summary: type: File outputSource: annotate_variants/vep_summary steps: haplotype_caller: run: gatk_haplotypecaller_iterator.cwl in: reference: reference cram: cram emit_reference_confidence: emit_reference_confidence gvcf_gq_bands: gvcf_gq_bands intervals: intervals contamination_fraction: contamination_fraction out: [gvcf] genotype_gvcfs: run: gatk_genotypegvcfs.cwl in: reference: reference gvcfs: haplotype_caller/gvcf out: [genotype_vcf] annotate_variants: run: vep.cwl in: vcf: genotype_gvcfs/genotype_vcf cache_dir: vep_cache_dir synonyms_file: synonyms_file coding_only: coding_only hgvs: hgvs_annotation reference: reference custom_gnomad_vcf: custom_gnomad_vcf out: [annotated_vcf, vep_summary] bgzip_annotated_vcf: run: bgzip.cwl in: file: annotate_variants/annotated_vcf out: [bgzipped_file] index_annotated_vcf: run: index_vcf.cwl in: vcf: bgzip_annotated_vcf/bgzipped_file out: [indexed_vcf] coding_variant_filter: run: filter_vcf_coding_variant.cwl in: vcf: annotate_variants/annotated_vcf out: [filtered_vcf] bgzip_coding_vcf: run: bgzip.cwl in: file: coding_variant_filter/filtered_vcf out: [bgzipped_file] index_coding_vcf: run: index_vcf.cwl in: vcf: bgzip_coding_vcf/bgzipped_file out: [indexed_vcf] limit_variants: run: select_variants.cwl in: reference: reference vcf: index_coding_vcf/indexed_vcf interval_list: limit_variant_intervals exclude_filtered: default: true out: [filtered_vcf]