#!/usr/bin/env cwl-runner
cwlVersion: v1.1
class: CommandLineTool
doc: string
requirements:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/bwa:0.7.17--h84994c4_5

baseCommand: [bwa, mem]

inputs:
  threads:
    type: int
    label: "number of threads"
    default: 4
    inputBinding:
      prefix: -t
  output_sam:
    type: string
    label: "sam file to output results to"
    default: "out.sam"
    inputBinding:
      prefix: -o
  group_header_line:
    type: string?
    label: "read group header line such as '@RG\tID:foo\tSM:bar'"
    inputBinding:
      prefix: -R
  index_base:
    type: File
    label: "fasta file for index basename"
    inputBinding:
      position: 1
    secondaryFiles:
      - .amb
      - .ann
      - .bwt
      - .pac
      - .sa
  fastq_forward:
    type: File
    label: "input fastq file to map (single-end or forward for pair-end)"
    inputBinding:
      position: 2
  fastq_reverse:
    type: File?
    label: "input fastq file to map (reverse for pair-end)"
    inputBinding:
      position: 3

outputs:
  output:
    type: File
    outputBinding:
      glob: "$(inputs.output_sam)"
  stdout: stdout
  stderr: stderr
stdout: bwa-mem-stdout.log
stderr: bwa-mem-stderr.log