doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml

   1 #!/usr/bin/env cwl-runner
   2 # Copyright (C) The Arvados Authors. All rights reserved.
   3 #
   4 # SPDX-License-Identifier: CC-BY-SA-3.0
   5
   6 # Example input file using UUIDs to reference input collections. These
   7 # will be resolved to content addresses before running the workflow.
   8
   9 $namespaces:
  10   arv: 'http://arvados.org/cwl#'
  11
  12 cwl:tool: bwa-mem.cwl
  13 reference:
  14   class: File
  15   location: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt
  16   arv:collectionUUID: qr1hi-4zz18-pwid4w22a40jp8l
  17 read_p1:
  18   class: File
  19   location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_1.fastq
  20   arv:collectionUUID: qr1hi-4zz18-h615rgfmqt3wje0
  21 read_p2:
  22   class: File
  23   location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_2.fastq
  24   arv:collectionUUID: qr1hi-4zz18-h615rgfmqt3wje0
  25 group_id: arvados_tutorial
  26 sample_id: HWI-ST1027_129
  27 PL: illumina