Welcome to the Workflows Quickstart Tutorial, Part 3. Learn how to run a downstream analysis on the output data you generated in Part 2 of the Workflows Quickstart.
Use workflow output data for downstream analysis
Setting up the workflow
- Choose the root entity type
- Select data
- Configure Inputs
- Configure Outputs and run the workflow
What to expect (successful submissions)
Workflow didn't succeed? Try these troubleshooting tips and tricks
Using workflow output data in downstream analysis
|What you will learn (how data tables can streamline and scale your analysis)
In part 3, you'll learn how data tables can simplify your analysis in two ways
You'll build on the first two exercises by configuring a workflow to use the outputs from
About the workflow
How much will it cost? How long will it take?
Right click to open the tutorial demo in a new tab
Setting up the workflow
Your goal is to run the Part 3 workflow on the output data in the set you created in Part 2.
Start by selecting the
Part3_BAM_to_unmappedBAM workflow. You'll be directed to the configuration form (see screenshot below). The parts you will need to complete are numbered. See if you can complete them on your own. Open the sections below for hints.
1. Choose the root entity type
The root entity type is "sample" because the outputs from the previous workflow were written to the sample table, where you will find them alongside the primary input data.
2. Select Data (run on the output of the two samples in the set from Part 2)
3. Configure Input data
3.1. In the input_bam attribute field, start typing
this. Select the output name you set up in Part 2 from the options in the dropdown.
Notice that the dropdown includes all columns in the "samples" data table, including those from Part 1! Be careful to select the name you used as output in Part 2.
3.2. Save your Inputs attributes by clicking on the blue Save button!
4. Configure the outputs and run the workflow
To write to the data table, start by typing "this." and then fill in a name for this attribute. The workflow will generate a column for the generated data in the sample table.
4.2. Save the Outputs
4.3. Click the blue Run Analysis button to submit your workflows
You will see the following popup
What to expect - successful submissions
Congratulations! You configured the inputs correctly and the workflow succeeded. You should see the green “succeeded” icon in the Job History:
If you go to the Data tab and expand the "sample" table, you will see the outputs under a new column (uBAM):
If you click on the "3 items" link, you'll notice that there are three output files for each sample, corresponding to how the workflow processes the data (by separate shards):
Workflow didn't succeed? Try these troubleshooting tips
This will lead you to a more detailed page. If you hover over the link in the Messages column, you'll get information that can help troubleshooting. In the case below, one of the submissions failed because it didn't find the input file. I was using the output name from Part 1, where I only ran the first sample.
For more tips, see this article.
Next up: PWorkflows-Quickstart -Part 4 - Advanced setup - Arrays and Pairs