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IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here
IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here
created by Tiffany_at_Broad
on 2018-01-03
Launching an analysis is pretty simple once you have the method inputs configured. This video demo shows how to launch an analysis with a Featured Workspace, where the methods are configured for you. The steps are detailed below.
- Click the Launch Analysis… button in the Method configuration tab.
- If you are not using the data model (i.e. you have unchecked the checkbox Configure inputs/outputs using the Workspace Data Model) then you can skip to Step 3. If you are using the data model, now you can select what sample, participant, pair, or set you want the method to run on. For example, if the Root entity type is equal to "sample," choose a sample. If you want the method to run on multiple samples, you will have to create a sample set and Define an Expression,
this.samples, that will expand the workflow from running on a single sample to multiple samples in the set. See the Defining Expressions section for more detail. Note: You can change the Root entity type of a method configuration, by selecting Edit Configuration... and choosing from the drop-down options. - Decide whether to turn call caching on or off.
- Click Launch. This starts a conversation between FireCloud, Cromwell, PAPI, and Dockerhub or other image registry. FireCloud will then take you to the Monitor tab, to monitor your submission and workflows.
Defining Expressions
Defining Expressions is most commonly required when you want to run on sets of participants, samples, or pairs instead of one item.
For example, see the screenshot below of the Test_data sample set with two samples. To get this method to run on both samples, you add the expression this.samples
See how samples is the name of the third column in the sampleset table? FireCloud reads this as, “run the method on whatever is in the samples column for the Testdata sample set.” One workflow will be created for each sample in the set and submitted all at once.
Updated on 2018-07-19
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