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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Avoid re-doing STAR references in RNAseq Germline variant workflow

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    Pamela Bretscher

    Hi ThyagoLC,

    I am going to move your post into our Community Discussions -> General Discussion topic, as the germline topic is for reporting bugs with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.

    Best,

    Pamela

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    Samantha (she/her)

    Hi ThyagoLC,

    If you take a look at this line in the WDL, the StarGenerateReferences task runs if the input zippedStarReferences is undefined. So if you already have a reference file you'd like to use, you can pass that to the zippedStarReferences input.

    As for your second question, I'm not sure if this is the right forum for it. We support questions/issues related to Terra Cromwell, but not external/personal instances of Cromwell. Bioinformatics StackExchange and Cromwell Slack are the best resources for those questions.

    Best,

    Samantha

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    ThyagoLC

    Hi Samantha (she/her)

    I found out about the zippedStarReferences input later on, thank you!

    As for the second question, I'll leave my solution below so others may benefit from it:

    I used a custom .conf file to pass my user/group UID:GID to docker in the following place:

    cromwell.examples.conf

    Then, just ran the custom.conf to my call

    java -Dconfig.file=/path/to/custom.conf cromwell.jar ...

    Thank you.

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    Samantha (she/her)

    Hi ThyagoLC,

    Thanks for following up and posting your solution!

    Best,

    Samantha

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