hints:
DockerRequirement:
- dockerPull: lh3lh3/bwa
+ dockerPull: quay.io/biocontainers/bwa:0.7.17--ha92aebf_3
-baseCommand: [mem]
+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: