X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b8ffcc224f73c5c856c6d5993ba06255892a789f..33b27555b25e70a0d37c5a8267450fddf3bd81b1:/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 2001971264..018867c83e 100755
--- 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:
-    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: