15964: Update and reorganize keep & CWL user guide docs

[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 a73329288c7cee58e699a016f5a020360d7d10ad..018867c83e29bdf04bb6d54173e86f059c192d0c 100755 (executable)
--- a/doc/user/cwl/bwa-mem/bwa-mem.cwl
+++ b/doc/user/cwl/bwa-mem/bwa-mem.cwl
@@ -10,11 +10,11 @@ hints:
   DockerRequirement:
     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: