-~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --create-workflow bwa-mem.cwl
+~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --project-uuid zzzzz-j7d0g-p32bi47ogkjke11 --create-workflow bwa-mem.cwl
arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Upload local files: "bwa-mem.cwl"
2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Uploaded to zzzzz-4zz18-7e0hedrmkuyoei3
@@ -134,7 +146,7 @@ zzzzz-p5p6p-rjleou1dwr167v5
You can provide a partial input file to set default values for the workflow input parameters. You can also use the @--name@ option to set the name of the workflow:
-~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --name "My workflow with defaults" --create-workflow bwa-mem.cwl bwa-mem-template.yml
+~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --name "My workflow with defaults" --project-uuid zzzzz-j7d0g-p32bi47ogkjke11 --create-workflow bwa-mem.cwl bwa-mem-template.yml
arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Upload local files: "bwa-mem.cwl"
2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Uploaded to zzzzz-4zz18-0f91qkovk4ml18o
@@ -143,6 +155,20 @@ zzzzz-p5p6p-zuniv58hn8d0qd8
+Use @--update-workflow @ to update an existing workflow.
+
+
+~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --update-workflow zzzzz-p5p6p-zuniv58hn8d0qd8 bwa-mem.cwl
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Upload local files: "bwa-mem.cwl"
+2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Uploaded to zzzzz-4zz18-7e0hedrmkuyoei3
+2016-07-01 12:21:01 arvados.cwl-runner[15796] INFO: Created template zzzzz-p5p6p-zuniv58hn8d0qd8
+zzzzz-p5p6p-zuniv58hn8d0qd8
+
+
+
+When using @--create-workflow@ or @--update-workflow@, the @--copy-deps@ and @--match-submitter-images@ options are enabled by default.
+
h3. Running registered workflows at the command line
You can run a registered workflow at the command line by its UUID: