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 providing both content addresses and UUIDs.  The
   7 # collections identified by 'collectionUUID' will be checked that the
   8 # current content of the collection record matches the content address
   9 # in the 'location' field.
  10
  11 $namespaces:
  12   arv: 'http://arvados.org/cwl#'
  13
  14 cwl:tool: bwa-mem.cwl
  15 reference:
  16   class: File
  17   location: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt
  18   arv:collectionUUID: jutro-4zz18-tv416l321i4r01e
  19 read_p1:
  20   class: File
  21   location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_1.fastq
  22   arv:collectionUUID: jutro-4zz18-8k5hsvee0izv2g3
  23 read_p2:
  24   class: File
  25   location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_2.fastq
  26   arv:collectionUUID: jutro-4zz18-8k5hsvee0izv2g3
  27 group_id: arvados_tutorial
  28 sample_id: HWI-ST1027_129
  29 PL: illumina