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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 b5c9f82a1a5f79970a97e92d91fce7de9268430c..018867c83e29bdf04bb6d54173e86f059c192d0c 100755
(executable)
--- a/
doc/user/cwl/bwa-mem/bwa-mem.cwl
+++ b/
doc/user/cwl/bwa-mem/bwa-mem.cwl
@@
-8,13
+8,13
@@
class: CommandLineTool
hints:
DockerRequirement:
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: