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layout: default
navsection: userguide
title: "Running a pipeline using Workbench"
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A "pipeline" (sometimes called a "workflow" in other systems) is sequence of steps that apply various programs or tools to transform input data to output data. Pipelines are the principal means of performing computation with Arvados. This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from an sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file. This will introduce the following Arvados features:
* How to create a project.
* How to browse available pipeline templates and create a new pipeline from an existing template.
* How to browse and select input data for the pipeline and submit the pipeline to run on the Arvados cluster.
* How to access your pipeline results.
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# Start from the *Workbench Dashboard*. You can return to the dashboard by clicking on * Home* in the upper left corner of any Workbench page.
# Click on Add new project on the "My projects" panel. This will direct you to the page for the new project.
# On the new project page, click on the pencil icon next to *New project* to pop up a text box and change the project title to *Tutorial output*. Click on to save the new name.
# Click on Run a pipeline... This will open a modal dialog box titled *Choose a pipeline to run*.
# Click on * Projects *. Under *Projects shared with me* select * Arvados Tutorial*.
# Select * Tutorial align using bwa mem* and click on Next: choose inputs . This will load a new page where you will supply the inputs for the pipeline.
# Click on Choose under the first input parameter to the pipeline *reference_collection*. This will open a modal dialog box titled *Choose a dataset*.
# Once again click on * Projects * and under *Projects shared with me* select * Arvados Tutorial*. Select * Tutorial chromosome 19 reference* and click on OK.
# Repeat the previous step to supply the *sample* parameter, this time choosing * Tutorial sample exome*.
# Click on Run .
# This will refresh the page. The pipeline will be queued and shortly start running. You can track the progress by watching log messages from jobs. This page refreshes automatically. You will see success under the *job* the column when the pipeline completes successfully.
# Click on * Show output files* to see the results of the job. This will load a new page listing the output files from this pipeline. Under the *Files* tab will be the output SAM file from the alignment tool
# Click on the download icon to the right of the SAM file download your results.
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