---
layout: default
navsection: userguide
title: "Starting a Workflow at the Command Line"
...
{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.

SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}

{% include 'what_is_cwl' %}

{% include 'tutorial_expectations' %}

This tutorial will demonstrate how to submit a workflow at the command line using @arvados-cwl-runner@.

# "Get the tutorial files":#get-files
# "Submitting a workflow to an Arvados cluster":#submitting
# "Registering a workflow to use in Workbench":#registering
# "Make a workflow file directly executable":#executable

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

<notextile>
<pre><code>~$ <span class="userinput">git clone https://git.arvados.org/arvados.git</span>
~$ <span class="userinput">cd arvados/doc/user/cwl/bwa-mem</span>
</code></pre>
</notextile>

The tutorial data is hosted on "https://playground.arvados.org":https://playground.arvados.org (also referred to by the identifier *pirca*).  If you are using a different Arvados instance, you may need to copy the data to your own instance.  One way to do this is with "arv-copy":{{site.baseurl}}/user/topics/arv-copy.html (this requires signing up for a free playground.arvados.org account).

<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src pirca --dst settings 2463fa9efeb75e099685528b3b9071e0+438</span>
~$ <span class="userinput">arv-copy --src pirca --dst settings ae480c5099b81e17267b7445e35b4bc7+180</span>
</code></pre>
</notextile>

If you do not wish to create an account on "https://playground.arvados.org":https://playground.arvados.org, you may download the files anonymously and upload them to your local Arvados instance:

"https://collections.pirca.arvadosapi.com/c=2463fa9efeb75e099685528b3b9071e0+438/":https://collections.pirca.arvadosapi.com/c=2463fa9efeb75e099685528b3b9071e0+438/

"https://collections.pirca.arvadosapi.com/c=ae480c5099b81e17267b7445e35b4bc7+180/":https://collections.pirca.arvadosapi.com/c=ae480c5099b81e17267b7445e35b4bc7+180/

h2(#submitting). Submitting a workflow to an Arvados cluster

h3. Submit a workflow and wait for results

Use @arvados-cwl-runner@ to submit CWL workflows to Arvados.  After submitting the job, it will wait for the workflow to complete and print out the final result to standard output.

*Note:* Once submitted, the workflow runs entirely on Arvados, so even if you log out, the workflow will continue to run.  However, if you interrupt @arvados-cwl-runner@ with control-C it will cancel the workflow.

<notextile>
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner 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
2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
{
    "aligned_sam": {
        "location": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
        "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
        "class": "File",
        "size": 30738986
    }
}
</code></pre>
</notextile>

h3. Referencing files

When running a workflow on an Arvados cluster, the input files must be stored in Keep.  There are several ways this can happen.

A URI reference to Keep uses the @keep:@ scheme followed by either the portable data hash or UUID of the collection and then the location of the file inside the collection.  For example, @keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@ or @keep:zzzzz-4zz18-zzzzzzzzzzzzzzz/19.fasta.bwt@.

If you reference a file in "arv-mount":{{site.baseurl}}/user/tutorials/tutorial-keep-mount-gnu-linux.html, such as @/home/example/keep/by_id/2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@, then @arvados-cwl-runner@ will automatically determine the appropriate Keep URI reference.

If you reference a local file which is not in @arv-mount@, then @arvados-cwl-runner@ will upload the file to Keep and use the Keep URI reference from the upload.

You can also execute CWL files that have been uploaded Keep:

<notextile>
<pre><code>
~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-put --portable-data-hash --name "bwa-mem.cwl" bwa-mem.cwl</span>
2020-08-20 13:40:02 arvados.arv_put[12976] INFO: Collection saved as 'bwa-mem.cwl'
f141fc27e7cfa7f7b6d208df5e0ee01b+59
~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner keep:f141fc27e7cfa7f7b6d208df5e0ee01b+59/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: 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
2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
{
    "aligned_sam": {
        "location": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
        "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
        "class": "File",
        "size": 30738986
    }
}
</code></pre>
</notextile>

Note: uploading a workflow file to Keep is _not_ the same as registering the workflow for use in Workbench.  See "Registering a workflow to use in Workbench":#registering below.

h3. Work reuse

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. 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.

<notextile>
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --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
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" --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>

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
2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
{
    "aligned_sam": {
        "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
        "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
        "class": "File",
        "size": 30738986
    }
}
</code></pre>
</notextile>

You can even make an input file directly executable the same way with the following two lines at the top:

<notextile>
<pre><code>#!/usr/bin/env cwl-runner
cwl:tool: <span class="userinput">bwa-mem.cwl</span>
</code></pre>
</notextile>

<notextile>
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">./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
2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
{
    "aligned_sam": {
        "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
        "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
        "class": "File",
        "size": 30738986
    }
}
</code></pre>
</notextile>

h2(#setup). Setting up arvados-cwl-runner

See "Arvados CWL Runner":{{site.baseurl}}/sdk/python/arvados-cwl-runner.html