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

# Example input file using UUIDs to reference input collections. These
# will be resolved to content addresses before running the workflow.

$namespaces:
  arv: 'http://arvados.org/cwl#'

cwl:tool: bwa-mem.cwl
reference:
  class: File
  location: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt
  arv:collectionUUID: qr1hi-4zz18-pwid4w22a40jp8l
read_p1:
  class: File
  location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_1.fastq
  arv:collectionUUID: qr1hi-4zz18-h615rgfmqt3wje0
read_p2:
  class: File
  location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_2.fastq
  arv:collectionUUID: qr1hi-4zz18-h615rgfmqt3wje0
group_id: arvados_tutorial
sample_id: HWI-ST1027_129
PL: illumina