[ARVADOS] updated: 1.1.2-2-gb3efaa3

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Summary of changes:
 doc/user/cwl/bwa-mem/bwa-mem.cwl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

       via  b3efaa37f1e3c52b5a126ba3416856ceba21549a (commit)
       via  b8ffcc224f73c5c856c6d5993ba06255892a789f (commit)
      from  71940143887b6b97ca358cef5a815d0f7a848f49 (commit)

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commit b3efaa37f1e3c52b5a126ba3416856ceba21549a
Merge: 7194014 b8ffcc2
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date:   Thu Dec 21 11:53:26 2017 -0500

    Merge branch 'patch-2' of https://github.com/jrandall/arvados
    
    fixes #11621
    
    Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>


commit b8ffcc224f73c5c856c6d5993ba06255892a789f
Author: Joshua C. Randall <jcrandall at alum.mit.edu>
Date:   Thu Dec 21 14:54:13 2017 +0000

    fix bwa-mem.cwl docker repo
    
    Change from missing `biodckr/bwa` repo to minimal bwa docker image `lh3lh3/bwa`
    The new docker image has `bwa` set as entrypoint, so also change `baseCommand` from `[bwa, mem]` to `[mem]`
    Fixes 11621
    
    Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall at alum.mit.edu>

diff --git a/doc/user/cwl/bwa-mem/bwa-mem.cwl b/doc/user/cwl/bwa-mem/bwa-mem.cwl
index b5c9f82..2001971 100755
--- a/doc/user/cwl/bwa-mem/bwa-mem.cwl
+++ b/doc/user/cwl/bwa-mem/bwa-mem.cwl
@@ -8,9 +8,9 @@ class: CommandLineTool
 
 hints:
   DockerRequirement:
-    dockerPull: biodckr/bwa
+    dockerPull: lh3lh3/bwa
 
-baseCommand: [bwa, mem]
+baseCommand: [mem]
 
 arguments:
   - {prefix: "-t", valueFrom: $(runtime.cores)}

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