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21504: Add an `arv-mount --exec` example
[arvados.git]
/
doc
/
user
/
cwl
/
bwa-mem
/
bwa-mem.cwl
diff --git
a/doc/user/cwl/bwa-mem/bwa-mem.cwl
b/doc/user/cwl/bwa-mem/bwa-mem.cwl
index ba3b6a0e897e69fc2bce2464302a2f3c6ff70043..018867c83e29bdf04bb6d54173e86f059c192d0c 100755
(executable)
--- a/
doc/user/cwl/bwa-mem/bwa-mem.cwl
+++ b/
doc/user/cwl/bwa-mem/bwa-mem.cwl
@@
-1,16
+1,20
@@
#!/usr/bin/env cwl-runner
#!/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:
cwlVersion: v1.0
class: CommandLineTool
hints:
DockerRequirement:
- dockerPull:
biodckr/bwa
+ dockerPull:
quay.io/biocontainers/bwa:0.7.17--ha92aebf_3
baseCommand: [bwa, mem]
arguments:
- {prefix: "-t", valueFrom: $(runtime.cores)}
baseCommand: [bwa, mem]
arguments:
- {prefix: "-t", valueFrom: $(runtime.cores)}
- - {prefix: "-R", valueFrom:
"@RG\tID:$(inputs.group_id)\tPL:$(inputs.PL)\tSM:$(inputs.sample_id)"
}
+ - {prefix: "-R", valueFrom:
'@RG\\\tID:$(inputs.group_id)\\\tPL:$(inputs.PL)\\\tSM:$(inputs.sample_id)'
}
inputs:
reference:
inputs:
reference: