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Samtofastq Method Config.

I am new to FireCloud. I was wondering if it is possible to revert BAMs to FASTQ, then merge multiple FASTQ from different runs for one sample, and then align back - all in FireCloud. I first tried the existent Samtofastq method configuration on FireCloud but I don't seem to be able to write the appropriate metadata file to run it because I cannot find how to write it up. I do not want to write my own WDL, I just want to use the method configuration that exists already.
Thank you in advance for any help.


  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    I would recommend reading through our Quickstart Guide if you are not already familiar with FireCloud as a platform. It helps to walk you through the parts of the platform, so you can orient yourself.

    In order to use an existent method in the method repository, you can follow the below tutorials:
    (howto) Create a workspace
    (howto) Import metadata <- This one specifically covers how to write an appropriate metadata file under the section "Importing a file".

    Then, if you have access to an existing method configuration, you can simply import that configuration into your workspace, and run it.

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