#!/usr/bin/env cwl-runner
# Copyright (C) The Arvados Authors. All rights reserved.
#
# SPDX-License-Identifier: CC-BY-SA-3.0

cwlVersion: v1.0
class: CommandLineTool

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/bwa:0.7.17--ha92aebf_3

baseCommand: [bwa, mem]

arguments:
  - {prefix: "-t", valueFrom: $(runtime.cores)}
  - {prefix: "-R", valueFrom: '@RG\\\tID:$(inputs.group_id)\\\tPL:$(inputs.PL)\\\tSM:$(inputs.sample_id)'}

inputs:
  reference:
    type: File
    inputBinding:
      position: 1
      valueFrom: $(self.dirname)/$(self.nameroot)
    secondaryFiles:
      - ^.ann
      - ^.amb
      - ^.pac
      - ^.sa
    doc: The index files produced by `bwa index`
  read_p1:
    type: File
    inputBinding:
      position: 2
    doc: The reads, in fastq format.
  read_p2:
    type: File?
    inputBinding:
      position: 3
    doc:  For mate paired reads, the second file (optional).
  group_id: string
  sample_id: string
  PL: string

stdout: $(inputs.read_p1.nameroot).sam

outputs:
  aligned_sam:
    type: stdout