Merge branch '15397-remove-obsolete-apis'

[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
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: CC-BY-SA-3.0
+
 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: $(runtime.cores)}
-  - {prefix: "-R", valueFrom: "@RG\tID:$(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: