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layout: default
navsection: userguide
title: "Writing a pipeline template"
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This tutorial demonstrates how to construct a two stage pipeline template that uses the "bwa mem":http://bio-bwa.sourceforge.net/ tool to produce a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file, then uses the "Picard SortSam tool":http://picard.sourceforge.net/command-line-overview.shtml#SortSam to produce a BAM (Binary Alignment/Map) file.

{% include 'tutorial_expectations' %}

Use the following command to create an empty template using @arv create pipeline_template@:

<notextile>
<pre><code>~$ <span class="userinput">arv create pipeline_template</span></code></pre>
</notextile>

This will open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@).  Now, update the contents of the editor with the following content:

<notextile>{% code 'tutorial_bwa_sortsam_pipeline' as javascript %}</notextile>

* @"name"@ is a human-readable name for the pipeline.
* @"components"@ is a set of scripts or commands that make up the pipeline.  Each component is given an identifier (@"bwa-mem"@ and @"SortSam"@) in this example).
** Each entry in components @"components"@ is an Arvados job submission.  For more information about individual jobs, see the "job object reference":{{site.baseurl}}/api/schema/Job.html and "job create method.":{{site.baseurl}}/api/methods/jobs.html#create
* @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados.  These parameters are described in more detail in "Writing a script":tutorial-firstscript.html.
* @"runtime_constraints"@ describes runtime resource requirements for the component.
** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job.  The Docker image @"bcosc/arv-base-java"@ supplied here has the Java runtime environment, bwa, and samtools installed.
** @"arvados_sdk_version"@ specifies a version of the Arvados SDK to load alongside the job's script.
* @"script_parameters"@ describes the component parameters.
** @"command"@ is the actual command line to invoke the @bwa@ and then @SortSam@.  The notation @$()@ denotes macro substitution commands evaluated by the run-command tool wrapper.
** @"task.stdout"@ indicates that the output of this command should be captured to a file.
** @$(node.cores)@ evaluates to the number of cores available on the compute node at time the command is run.
** @$(tmpdir)@ evaluates to the local path for temporary directory the command should use for scratch data.
** @$(reference_collection)@ evaluates to the script_parameter @"reference_collection"@
** @$(dir $(...))@ constructs a local path to a directory representing the supplied Arvados collection.
** @$(file $(...))@ constructs a local path to a given file within the supplied Arvados collection.
** @$(glob $(...))@ searches the specified path based on a file glob pattern and evalutes to the first result.
** @$(basename $(...))@ evaluates to the supplied path with leading path portion and trailing filename extensions stripped
* @"output_of"@ indicates that the @output@ of the @bwa-mem@ component should be used as the @"input"@ script parameter of @SortSam@.  Arvados uses these dependencies between components to automatically determine the correct order to run them.

When using @run-command@, the tool should write its output to the current working directory.  The output will be automatically uploaded to Keep when the job completes.

See the "run-command reference":{{site.baseurl}}/user/topics/run-command.html for more information about using @run-command@.

h2. Running your pipeline

Your new pipeline template should appear at the top of the Workbench "pipeline&nbsp;templates":{{site.arvados_workbench_host}}/pipeline_templates page.  You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html

Test data is available in the "Arvados Tutorial":{{site.arvados_workbench_host}}/projects/qr1hi-j7d0g-u7zg1qdaowykd8d project:

* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":{{site.arvados_workbench_host}}/collections/2463fa9efeb75e099685528b3b9071e0+438 for the "reference_collection" parameter
* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":{{site.arvados_workbench_host}}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter

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