class: Workflow cwlVersion: v1.0 hints: [] inputs: - id: batch_rec type: items: fields: - name: description type: string - name: config__algorithm__validate type: File - name: reference__fasta__base type: File - name: config__algorithm__variantcaller type: string - name: config__algorithm__coverage_interval type: string - name: metadata__batch type: 'null' - name: config__algorithm__validate_regions type: File - name: genome_build type: string - name: metadata__phenotype type: string - name: config__algorithm__tools_off type: items: string type: array - name: genome_resources__variation__dbsnp type: File - name: genome_resources__variation__cosmic type: 'null' - name: reference__genome_context type: items: File type: array - name: analysis type: string - name: config__algorithm__tools_on type: items: string type: array - name: config__algorithm__variant_regions type: File - name: reference__rtg type: File - name: align_bam type: File - name: regions__sample_callable type: File - name: config__algorithm__callable_regions type: File name: batch_rec type: record type: array outputs: - id: vc_rec outputSource: compare_to_rm/vc_rec type: items: fields: - name: validate__summary type: - File - 'null' - name: validate__tp type: - File - 'null' - name: validate__fp type: - File - 'null' - name: validate__fn type: - File - 'null' - name: description type: string - name: vrn_file type: File - name: config__algorithm__validate type: File - name: reference__fasta__base type: File - name: config__algorithm__variantcaller type: string - name: config__algorithm__coverage_interval type: string - name: metadata__batch type: 'null' - name: config__algorithm__validate_regions type: File - name: genome_build type: string - name: metadata__phenotype type: string - name: config__algorithm__tools_off type: items: string type: array - name: genome_resources__variation__dbsnp type: File - name: genome_resources__variation__cosmic type: 'null' - name: reference__genome_context type: items: File type: array - name: analysis type: string - name: config__algorithm__tools_on type: items: string type: array - name: config__algorithm__variant_regions type: File - name: reference__rtg type: File - name: align_bam type: File - name: regions__sample_callable type: File - name: config__algorithm__callable_regions type: File name: vc_rec type: record type: array requirements: - class: EnvVarRequirement envDef: - envName: MPLCONFIGDIR envValue: . - class: ScatterFeatureRequirement - class: SubworkflowFeatureRequirement steps: - id: get_parallel_regions in: - id: batch_rec source: batch_rec out: - id: region run: steps/get_parallel_regions.cwl - id: variantcall_batch_region in: - id: batch_rec source: batch_rec - id: region_toolinput source: get_parallel_regions/region out: - id: vrn_file_region - id: region run: steps/variantcall_batch_region.cwl scatter: - region_toolinput scatterMethod: dotproduct - id: concat_batch_variantcalls in: - id: batch_rec source: batch_rec - id: region source: variantcall_batch_region/region - id: vrn_file_region source: variantcall_batch_region/vrn_file_region out: - id: vrn_file run: steps/concat_batch_variantcalls.cwl - id: postprocess_variants in: - id: batch_rec source: batch_rec - id: vrn_file_toolinput source: concat_batch_variantcalls/vrn_file out: - id: vrn_file run: steps/postprocess_variants.cwl - id: compare_to_rm in: - id: batch_rec source: batch_rec - id: vrn_file source: postprocess_variants/vrn_file out: - id: vc_rec run: steps/compare_to_rm.cwl