#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow inputs: p1: type: File[]? description: list of files containing the first end of paired end reads in fasta or fastq format p2: type: File[]? description: list of files containing the second end of paired end reads in fasta or fastq format output_prefix: type: string description: prefix for output files. will output prefix.aligned.bam and prefix.aligned.stats reference: type: File description: "lobSTR's bwa reference files" rg-sample: type: string description: Use this in the read group SM tag rg-lib: type: string description: Use this in the read group LB tag strinfo: type: File description: File containing statistics for each STR. noise_model: type: File description: File to read noise model parameters from (.stepmodel) secondaryFiles: - "^.stuttermodel" outputs: bam: type: File outputSource: samindex/bam_with_bai bam_stats: type: File outputSource: lobSTR/bam_stats vcf: type: File outputSource: allelotype/vcf vcf_stats: type: File outputSource: allelotype/vcf_stats hints: DockerRequirement: dockerPull: rabix/lobstr steps: lobSTR: run: lobSTR-tool.cwl in: p1: p1 p2: p2 output_prefix: output_prefix reference: reference rg-sample: rg-sample rg-lib: rg-lib out: [bam, bam_stats] samsort: run: samtools-sort.cwl in: input: lobSTR/bam output_name: {default: "aligned.sorted.bam" } out: [output_file] samindex: run: samtools-index.cwl in: input: samsort/output_file out: [bam_with_bai] allelotype: run: allelotype.cwl in: bam: samindex/bam_with_bai reference: reference output_prefix: output_prefix noise_model: noise_model strinfo: strinfo out: [vcf, vcf_stats]