---
layout: default
navsection: userguide
title: "Writing a multi-step pipeline"
...

A pipeline in Arvados is a collection of crunch scripts, in which the output from one script may be used as the input to another script.

*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*

This tutorial uses *@you@* to denote your username.  Replace *@you@* with your user name in all the following examples.

h2. Create a new script

Our second script will filter the output of @hash.py@ and only include hashes that start with 0.  Create a new script in <notextile><code>~/<b>you</b>/crunch_scripts/</code></notextile> called @0-filter.py@:

<notextile> {% code '0_filter_py' as python %} </notextile>

Now add it to your repository:

<notextile>
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x 0-filter.py</span>
~/<b>you</b>/crunch_scripts$ <span class="userinput">git add 0-filter.py</span>
~/<b>you</b>/crunch_scripts$ <span class="userinput">git commit -m"zero filter"</span>
~/<b>you</b>/crunch_scripts$ <span class="userinput">git push origin master</span>
</code></pre>
</notextile>

h2. Create a pipeline template

Next, create a file that contains the pipeline definition:

<notextile>
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat &gt;~/the_pipeline &lt;&lt;EOF
{
  "name":"Filter MD5 hash values",
  "components":{
    "do_hash":{
      "script":"hash.py",
      "script_parameters":{
        "input":{
          "required": true,
          "dataclass": "Collection"
        }
      },
      "repository":"$USER",
      "script_version":"master",
      "output_is_persistent":false
    },
    "do_filter":{
      "script":"0-filter.py",
      "script_parameters":{
        "input":{
          "output_of":"do_hash"
        }
      },
      "repository":"$USER",
      "script_version":"master",
      "output_is_persistent":true
    }
  }
}
EOF
</span></code></pre>
</notextile>

* @"output_of"@ indicates that the @output@ of the @do_hash@ component should be used as the @"input"@ of @do_filter@.  Arvados uses these dependencies between jobs to automatically determine the correct order to run them.

(Your shell should automatically fill in @$USER@ with your login name.  The JSON that gets saved should have @"repository"@ pointed at your personal Git repository.)

Now, use @arv pipeline_template create@ to register your pipeline template in Arvados:

<notextile>
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat ~/the_pipeline)"</span>
</code></pre>
</notextile>

Your new pipeline template will appear on the Workbench "Compute %(rarr)&rarr;% Pipeline&nbsp;templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page.

For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html