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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

Error using a edited gatk wdl (bam-unmapped-bam workflow) to accept array[files] as input rather than a single .bam file

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    Bhanu Gandham

    Hi sahuno

     

    This is a Terra/WDL question and not a GATK one. I have let the team know and someone from that WDL team will be in touch shortly.

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    Tiffany Miller

    Hey sahuno ! I'll need to take a closer look at this, but at first glance, I think you'll want to move that scatter above the RevertSam call in your workflow (between last input and call RevertSam) because it is an Array. It could look something like this:

     
     

    scatter (bams in flowcell_bams0) {

    ...

    }

     

    call RevertSam {

     

    input:

     

    input_bam = bams,

       
       

    Similar to this:

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    Tiffany Miller

    sahuno were you able to get it to work? Are you modifying this and running in Terra?

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