#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.0 requirements: - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement inputs: reference: type: File doc: reference human genome file indel_mode: type: string default: 'INDEL' snp_mode: type: string default: 'SNP' snpf_genome: type: string snpf_nodownload: type: boolean snpf_data_dir: type: Directory resource_mills: type: File haplotest_vcf: type: File resource_hapmap: type: File resource_omni: type: File resource_dbsnp: type: File outputs: recal_File: type: File outputSource: vqsr_snps/recal_File annotated_snps: type: File outputSource: snpeff_snps/annotated_vcf steps: vqsr_snps: run: ../../tools/GATK-VariantRecalibrator-SNPs.cwl in: haplotypecaller_snps_vcf: haplotest_vcf reference: reference resource_dbsnp: resource_dbsnp resource_omni: resource_omni resource_hapmap: resource_hapmap out: [tranches_File, recal_File] apply_recalibration_snps: run: ../../tools/GATK-ApplyRecalibration.cwl in: #raw_vcf: HaplotypeCaller/output_HaplotypeCaller raw_vcf: haplotest_vcf reference: reference recal_file: vqsr_snps/recal_File tranches_file: vqsr_snps/tranches_File mode: snp_mode out: [ vqsr_vcf ] snpeff_snps: run: ../../tools/snpEff.cwl in: genome: snpf_genome variant_calling_file: apply_recalibration_snps/vqsr_vcf nodownload: snpf_nodownload data_dir: snpf_data_dir out: [ annotated_vcf ]