h2(#get-files). Get the tutorial files
-The tutorial files are located in the documentation section of the Arvados source repository, which can be found on "git.arvados.org":https://git.arvados.org/arvados.git/tree/HEAD:/doc/user/cwl/bwa-mem or "github":https://github.com/arvados/arvados/tree/master/doc/user/cwl/bwa-mem
+The tutorial files are located in the documentation section of the Arvados source repository, which can be found on "git.arvados.org":https://git.arvados.org/arvados.git/tree/HEAD:/doc/user/cwl/bwa-mem or "github":https://github.com/arvados/arvados/tree/main/doc/user/cwl/bwa-mem
<notextile>
<pre><code>~$ <span class="userinput">git clone https://git.arvados.org/arvados.git</span>
Workflows submitted with @arvados-cwl-runner@ will take advantage of Arvados job reuse. If you submit a workflow which is identical to one that has run before, it will short cut the execution and return the result of the previous run. This also applies to individual workflow steps. For example, a two step workflow where the first step has run before will reuse results for first step and only execute the new second step. You can disable this behavior with @--disable-reuse@.
+h3(#docker). Docker images
+
+Docker images referenced by the workflow must be uploaded to Arvados. This requires @docker@ to be installed and usable by the user running @arvados-cwl-runner@. If the image is not present in the local Docker instance, @arvados-cwl-runner@ will first attempt to pull the image using @docker pull@, then upload it.
+
+If there is already a Docker image in Arvados with the same name, it will use the existing image. In this case, the submitter will not use Docker.
+
+The @--match-submitter-images@ option will check the id of the image in the local Docker instance and compare it to the id of the image already in Arvados with the same name and tag. If they are different, it will choose the image matching the local image id, which will be uploaded it if necessary. This helpful for development, if you locally rebuild the image with the 'latest' tag, the @--match-submitter-images@ will ensure that the newer version is used.
+
+h3(#dependencies). Dependencies
+
+Dependencies include collections and Docker images referenced by the workflow. Dependencies are automatically uploaded by @arvados-cwl-runner@ if they are not present or need to be updated. When running a workflow, dependencies that already exist somewhere on the Arvados instance (from a previous upload) will not be uploaded or copied, regardless of the project they are located in. Sometimes this creates problems when sharing a workflow run with others. In this case, use @--copy-deps@ to indicate that you want all dependencies to be copied into the destination project (specified by @--project-uuid@).
+
h3. Command line options
See "arvados-cwl-runner options":{{site.baseurl}}/user/cwl/cwl-run-options.html
h2(#registering). Registering a workflow to use in Workbench
-Use @--create-workflow@ to register a CWL workflow with Arvados. This enables you to share workflows with other Arvados users, and run them by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button on the Workbench Dashboard and on the command line by UUID.
+Use @--create-workflow@ to register a CWL workflow with Arvados. Use @--project-uuid@ to upload the workflow to a specific project, along with its dependencies. You can share the workflow with other Arvados users by sharing that project. You can run the workflow by clicking the <span class="btn btn-sm btn-primary">+ NEW</span> → <i class="fa fa-fw fa-gear"></i> *Run a process* menu items on the Workbench, and on the command line by UUID.
<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --create-workflow bwa-mem.cwl</span>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --project-uuid zzzzz-j7d0g-p32bi47ogkjke11 --create-workflow bwa-mem.cwl</span>
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
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:
<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --name "My workflow with defaults" --create-workflow bwa-mem.cwl bwa-mem-template.yml</span>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --name "My workflow with defaults" --project-uuid zzzzz-j7d0g-p32bi47ogkjke11 --create-workflow bwa-mem.cwl bwa-mem-template.yml</span>
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
</code></pre>
</notextile>
+Use @--update-workflow <uuid>@ to update an existing workflow.
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --update-workflow zzzzz-p5p6p-zuniv58hn8d0qd8 bwa-mem.cwl</span>
+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
+</code></pre>
+</notextile>
+
+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:
projects / arvados.git / blobdiff