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layout: default
navsection: userguide
title: Create a Workflow with Composer
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Copyright (C) The Arvados Authors. All rights reserved.

SPDX-License-Identifier: CC-BY-SA-3.0
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The Arvados Workflow Composer is a graphical interface for building Common Workflow Language (CWL) workflows to run on Arvados.

This tutorial will demonstrate:

# Creating a new git repository through Arvados to store the workflow
# Creating CommandLineTools for "sort" and "uniq"
# Creating a Workflow which uses "sort" and "uniq" to remove duplicate lines from a text file
# Submitting the Workflow to run on Arvados

h3. 1. Access from workbench

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h3. 2. Composer starting page

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h3. 3. Manage git repositories (opens Workbench in new tab)

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h3. 4. Add a new repository

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h3. 5. Return to Composer.  Use refresh button to discover new repository (may take a few moments to show up).

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h3. 6. Create a new Command Line Tool

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h3. 7. Set Docker image, base command, and input port for "sort" tool

The "Docker Repository" is the name:tag of a "Docker image uploaded Arvados.":{{site.baseurl}}/user/topics/arv-docker.html (Use @arv-keepdocker --pull debian:8@)  You can also find prepackaged bioinformatics tools on various sites, such as http://dockstore.org and http://biocontainers.pro/ .

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h3. 8. Redirect stdout to a file

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h3. 9. Capture output file

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h3. 10. Save Command Line Tool

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h3. 11. Repeat steps 6-10 for "uniq" tool

Create a new tool with a "base command" of "uniq".

h3. 12. Switch back to "Home" tab and create workflow

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h3. 13. Drag and drop tools into Workflow

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h3. 14. Drag from input port of "sort" to empty space to create workflow input

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h3. 15. Drag from output port of "sort" to input port of "uniq"

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h3. 16. Drag from output port of "uniq" to empty space to create workflow output

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h3. 17. Save Workflow

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h3. 18. Click on "Test" tab then click "Run"

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h3. 19. Choose input file

You may need to "upload an input file":{{site.baseurl}}/user/tutorials/tutorial-keep.html

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h3. 20. Run the workflow

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h3. 21. Monitor progress (may take several minutes)

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h3. 22. Get workflow output

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