#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow id: alignment-pair requirements: MultipleInputFeatureRequirement: {} ScatterFeatureRequirement: {} SubworkflowFeatureRequirement: {} InlineJavascriptRequirement: {} inputs: pair: type: type: array items: type: record fields: CN: string LB: string ID: string PL: string PU: string[] R1: File[] R2: File[] zR1: File[] zR2: File[] bam: File[] RG_ID: string[] adapter: string adapter2: string bwa_output: string genome: string intervals: string[] opt_dup_pix_dist: string hapmap: type: File secondaryFiles: - .idx dbsnp: type: File secondaryFiles: - .idx indels_1000g: type: File secondaryFiles: - .idx snps_1000g: type: File secondaryFiles: - .idx covariates: string[] abra_ram_min: int gatk_jar_path: string bait_intervals: File target_intervals: File fp_intervals: File ref_fasta: type: File secondaryFiles: - .amb - .ann - .bwt - .pac - .sa - .fai - ^.dict mouse_fasta: type: File secondaryFiles: - .amb - .ann - .bwt - .pac - .sa - .fai - ^.dict conpair_markers_bed: string outputs: bams: type: File[] secondaryFiles: - ^.bai outputSource: realignment/outbams clstats1: type: type: array items: type: array items: File outputSource: sample_alignment/clstats1 clstats2: type: type: array items: type: array items: File outputSource: sample_alignment/clstats2 md_metrics: type: File[] outputSource: sample_alignment/md_metrics as_metrics: type: File[] outputSource: sample_alignment/as_metrics hs_metrics: type: File[] outputSource: sample_alignment/hs_metrics insert_metrics: type: File[] outputSource: sample_alignment/insert_metrics insert_pdf: type: File[] outputSource: sample_alignment/insert_pdf per_target_coverage: type: File[] outputSource: sample_alignment/per_target_coverage doc_basecounts: type: File[] outputSource: sample_alignment/doc_basecounts gcbias_pdf: type: File[] outputSource: sample_alignment/gcbias_pdf gcbias_metrics: type: File[] outputSource: sample_alignment/gcbias_metrics gcbias_summary: type: File[] outputSource: sample_alignment/gcbias_summary conpair_pileup: type: File[] outputSource: sample_alignment/conpair_pileup covint_list: type: File outputSource: realignment/covint_list bed: type: File outputSource: realignment/covint_bed qual_metrics: type: File[] outputSource: realignment/qual_metrics qual_pdf: type: File[] outputSource: realignment/qual_pdf steps: sample_alignment: run: ../../workflows/sample-workflow.cwl in: sample: pair genome: genome opt_dup_pix_dist: opt_dup_pix_dist gatk_jar_path: gatk_jar_path bait_intervals: bait_intervals target_intervals: target_intervals fp_intervals: fp_intervals ref_fasta: ref_fasta mouse_fasta: mouse_fasta conpair_markers_bed: conpair_markers_bed out: [clstats1,clstats2,bam,md_metrics,as_metrics,hs_metrics,insert_metrics,insert_pdf,per_target_coverage,doc_basecounts,gcbias_pdf,gcbias_metrics,gcbias_summary,conpair_pileup] scatter: [sample] scatterMethod: dotproduct realignment: run: realignment.cwl in: pair: pair bams: sample_alignment/bam hapmap: hapmap dbsnp: dbsnp indels_1000g: indels_1000g snps_1000g: snps_1000g covariates: covariates genome: genome ref_fasta: ref_fasta intervals: intervals abra_ram_min: abra_ram_min out: [outbams, covint_list, covint_bed, qual_metrics, qual_pdf]