Merge branch 'main' from workbench2.git
[arvados.git] / 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