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navsection: userguide
title: "Running a pipeline using Workbench"
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A "pipeline" (sometimes called a "workflow" in other systems) is a 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 a 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 tutorial will introduce the following Arvados features:
* How to 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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h3. Steps
# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on * Dashboard* in the upper left corner of any Workbench page.
# Click on the Run a pipeline... button. This will open a dialog box titled *Choose a pipeline to run*.
# In the search box, type in *Tutorial align using bwa mem*.
# Select * Tutorial align using bwa mem* and click the Next: choose inputs button. This will create a new pipeline in your *Home* project and will open it. You can now supply the inputs for the pipeline.
# The first input parameter to the pipeline is *"reference_collection" parameter for run-command script in bwa-mem component*. Click the Choose button beneath that header. This will open a dialog box titled *Choose a dataset for "reference_collection" parameter for run-command script in bwa-mem component*.
# Open the *Home * menu and select *All Projects*. Search for and select * Tutorial chromosome 19 reference* and click the OK button.
# Repeat the previous two steps to set the *"sample" parameter for run-command script in bwa-mem component* parameter to * Tutorial sample exome*.
# Click on the Run button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster.
# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a complete label when the pipeline completes successfully.
# Click on the *Output* link to see the results of the job. This will load a new page listing the output files from this pipeline. You'll see the output SAM file from the alignment tool under the *Files* tab.
# Click on the download button to the right of the SAM file to download your results.
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