+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-rjleou1dwr167v5
+zzzzz-p5p6p-rjleou1dwr167v5
+</code></pre>
+</notextile>
+
+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" --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
+2016-07-01 14:09:50 arvados.cwl-runner[3730] INFO: Created template zzzzz-p5p6p-0deqe6nuuyqns2i
+zzzzz-p5p6p-zuniv58hn8d0qd8
+</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:
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner pirca-7fd4e-3nqbw08vtjl8ybz --help</span>
+INFO /home/peter/work/scripts/venv3/bin/arvados-cwl-runner 2.1.0.dev20200814195416, arvados-python-client 2.1.0.dev20200814195416, cwltool 3.0.20200807132242
+INFO Resolved 'pirca-7fd4e-3nqbw08vtjl8ybz' to 'arvwf:pirca-7fd4e-3nqbw08vtjl8ybz#main'
+usage: pirca-7fd4e-3nqbw08vtjl8ybz [-h] [--PL PL] [--group_id GROUP_ID]
+ [--read_p1 READ_P1] [--read_p2 READ_P2]
+ [--reference REFERENCE]
+ [--sample_id SAMPLE_ID]
+ [job_order]
+
+positional arguments:
+ job_order Job input json file
+
+optional arguments:
+ -h, --help show this help message and exit
+ --PL PL
+ --group_id GROUP_ID
+ --read_p1 READ_P1 The reads, in fastq format.
+ --read_p2 READ_P2 For mate paired reads, the second file (optional).
+ --reference REFERENCE
+ The index files produced by `bwa index`
+ --sample_id SAMPLE_ID
+</code></pre>
+</notextile>
+
+h2(#executable). Make a workflow file directly executable
+
+You can make a workflow file directly executable (@cwl-runner@ should be an alias to @arvados-cwl-runner@) by adding the following line to the top of the file:
+
+<notextile>
+<pre><code>#!/usr/bin/env cwl-runner
+</code></pre>
+</notextile>
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">./bwa-mem.cwl bwa-mem-input.yml</span>
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to zzzzz-4zz18-h7ljh5u76760ww2
+2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job zzzzz-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Running
+2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Complete