#!/usr/bin/env cwl-runner class: Workflow id: bam2gvcf-woBQSR-male label: bam2gvcf-woBQSR-male cwlVersion: v1.0 $namespaces: edam: 'http://edamontology.org/' requirements: SubworkflowFeatureRequirement: {} MultipleInputFeatureRequirement: {} inputs: reference: type: File format: edam:format_1929 doc: FastA file for reference genome secondaryFiles: - .fai - ^.dict reference_interval_name_autosome: type: string default: autosome doc: interval name for reference genome (autosome) reference_interval_list_autosome: type: File doc: interval list for reference genome (autosome) reference_interval_name_chrX: type: string default: chrX doc: interval name for reference genome (chrX) reference_interval_list_chrX: type: File doc: interval list for reference genome (chrX) reference_interval_name_chrY: type: string default: chrY doc: interval name for reference genome (chrY) reference_interval_list_chrY: type: File doc: interval list for reference genome (chrY) bam_files: type: File[] format: edam:format_2572 doc: array of input BAM alignment files (each file should be sorted) nthreads: type: int doc: number of cpu cores to be used outprefix: type: string doc: Output prefix name chrXY_outprefix: type: string doc: Output prefix name for chrXY steps: bams2gvcf_woBQSR: label: bams2gvcf_woBQSR doc: Call haplotypes from bam files run: ../Workflows/bams2gvcf.woBQSR.cwl in: bam_files: bam_files outprefix: outprefix reference: reference reference_interval_name_autosome: reference_interval_name_autosome reference_interval_list_autosome: reference_interval_list_autosome reference_interval_name_chrX: reference_interval_name_chrX reference_interval_list_chrX: reference_interval_list_chrX reference_interval_name_chrY: reference_interval_name_chrY reference_interval_list_chrY: reference_interval_list_chrY nthreads: nthreads out: - rmdup_bam - rmdup_metrics - rmdup_log - picard_collect_multiple_metrics_alignment_summary_metrics - picard_collect_multiple_metrics_insert_size_metrics - picard_collect_multiple_metrics_log - samtools_flagstat_flagstat - samtools_idxstats_idxstats - picard_CollectWgsMetrics_autosome_wgs_metrics - picard_CollectWgsMetrics_autosome_log - picard_CollectWgsMetrics_chrX_wgs_metrics - picard_CollectWgsMetrics_chrX_log - picard_CollectWgsMetrics_chrY_wgs_metrics - picard_CollectWgsMetrics_chrY_log - gatk3_HaplotypeCaller_vcf - gatk3_HaplotypeCaller_log gatk3_HaplotypeCaller_XCORE_ploidy1: label: gatk3_HaplotypeCaller_XCORE_ploidy1 doc: Call haplotypes for chrX core region with ploidy=1 run: ../Tools/gatk3-HaplotypeCaller-XCORE-ploidy1.cwl in: in_bam: bams2gvcf_woBQSR/rmdup_bam nthreads: nthreads reference: reference outprefix: outprefix out: [vcf, log] gatk3_HaplotypeCaller_Y_ploidy1: label: gatk3_HaplotypeCaller_Y_ploidy1 doc: Call haplotypes for chrY region with ploidy=1 run: ../Tools/gatk3-HaplotypeCaller-Y-ploidy1.cwl in: in_bam: bams2gvcf_woBQSR/rmdup_bam nthreads: nthreads reference: reference outprefix: outprefix out: [vcf, log] gatk3_SelectVariants_PAR1: label: gatk3_SelectVariants_PAR1 doc: Select variants for chrX PAR1 region run: ../Tools/gatk3-SelectVariants-PAR1.cwl in: vcf: bams2gvcf_woBQSR/gatk3_HaplotypeCaller_vcf nthreads: nthreads reference: reference outprefix: outprefix out: [out_vcf, log] gatk3_SelectVariants_PAR2: label: gatk3_SelectVariants_PAR2 doc: Select variants for chrX PAR2 region run: ../Tools/gatk3-SelectVariants-PAR2.cwl in: vcf: bams2gvcf_woBQSR/gatk3_HaplotypeCaller_vcf nthreads: nthreads reference: reference outprefix: outprefix out: [out_vcf, log] bcftools_concat: label: bcftools_concat doc: Concatenate VCF files run: ../Tools/bcftools-concat.cwl in: vcf_files: - gatk3_SelectVariants_PAR1/out_vcf - gatk3_HaplotypeCaller_XCORE_ploidy1/vcf - gatk3_SelectVariants_PAR2/out_vcf - gatk3_HaplotypeCaller_Y_ploidy1/vcf nthreads: nthreads outprefix: chrXY_outprefix out: [after_vcf] bcftools_index: label: bcftools_index doc: Make index for VCF file run: ../Tools/bcftools-index.cwl in: vcf: bcftools_concat/after_vcf nthreads: nthreads out: [vcf_tbi] outputs: rmdup_bam: type: File format: edam:format_2572 outputSource: bams2gvcf_woBQSR/rmdup_bam secondaryFiles: - ^.bai rmdup_metrics: type: File outputSource: bams2gvcf_woBQSR/rmdup_metrics rmdup_log: type: File outputSource: bams2gvcf_woBQSR/rmdup_log picard_collect_multiple_metrics_alignment_summary_metrics: type: File outputSource: bams2gvcf_woBQSR/picard_collect_multiple_metrics_alignment_summary_metrics secondaryFiles: - ^.bait_bias_detail_metrics - ^.bait_bias_summary_metrics - ^.base_distribution_by_cycle_metrics - ^.base_distribution_by_cycle.pdf - ^.error_summary_metrics - ^.gc_bias.detail_metrics - ^.gc_bias.pdf - ^.gc_bias.summary_metrics - ^.pre_adapter_detail_metrics - ^.pre_adapter_summary_metrics - ^.quality_by_cycle_metrics - ^.quality_by_cycle.pdf - ^.quality_distribution_metrics - ^.quality_distribution.pdf picard_collect_multiple_metrics_insert_size_metrics: type: File outputSource: bams2gvcf_woBQSR/picard_collect_multiple_metrics_insert_size_metrics secondaryFiles: - ^.insert_size_histogram.pdf picard_collect_multiple_metrics_log: type: File outputSource: bams2gvcf_woBQSR/picard_collect_multiple_metrics_log samtools_flagstat_flagstat: type: File outputSource: bams2gvcf_woBQSR/samtools_flagstat_flagstat samtools_idxstats_idxstats: type: File outputSource: bams2gvcf_woBQSR/samtools_idxstats_idxstats picard_CollectWgsMetrics_autosome_wgs_metrics: type: File outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_autosome_wgs_metrics picard_CollectWgsMetrics_autosome_log: type: File outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_autosome_log picard_CollectWgsMetrics_chrX_wgs_metrics: type: File outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrX_wgs_metrics picard_CollectWgsMetrics_chrX_log: type: File outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrX_log picard_CollectWgsMetrics_chrY_wgs_metrics: type: File outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrY_wgs_metrics picard_CollectWgsMetrics_chrY_log: type: File outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrY_log gatk3_HaplotypeCaller_vcf: type: File format: edam:format_3016 outputSource: bams2gvcf_woBQSR/gatk3_HaplotypeCaller_vcf secondaryFiles: - .tbi gatk3_HaplotypeCaller_log: type: File outputSource: bams2gvcf_woBQSR/gatk3_HaplotypeCaller_log gatk3_HaplotypeCaller_XCORE_ploidy1_vcf: type: File format: edam:format_3016 outputSource: gatk3_HaplotypeCaller_XCORE_ploidy1/vcf secondaryFiles: - .tbi gatk3_HaplotypeCaller_XCORE_ploidy1_log: type: File outputSource: gatk3_HaplotypeCaller_XCORE_ploidy1/log gatk3_HaplotypeCaller_Y_ploidy1_vcf: type: File format: edam:format_3016 outputSource: gatk3_HaplotypeCaller_Y_ploidy1/vcf secondaryFiles: - .tbi gatk3_HaplotypeCaller_Y_ploidy1_log: type: File outputSource: gatk3_HaplotypeCaller_Y_ploidy1/log gatk3_SelectVariants_PAR1_vcf: type: File format: edam:format_3016 outputSource: gatk3_SelectVariants_PAR1/out_vcf secondaryFiles: - .tbi gatk3_SelectVariants_PAR1_log: type: File outputSource: gatk3_SelectVariants_PAR1/log gatk3_SelectVariants_PAR2_vcf: type: File format: edam:format_3016 outputSource: gatk3_SelectVariants_PAR2/out_vcf secondaryFiles: - .tbi gatk3_SelectVariants_PAR2_log: type: File outputSource: gatk3_SelectVariants_PAR2/log bcftools_concat_vcf: type: File format: edam:format_3016 outputSource: bcftools_concat/after_vcf bcftools_index_vcf_tbi: type: File outputSource: bcftools_index/vcf_tbi