How to use same input directory and files in each Task of WDL pipeline on local system?

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Naser Elmi

• January 25, 2020 12:51

Hi, It is a general question regarding running GATK pipelines on a local cluster.

Each task of the wdl pipeline creates its own input files which can be time and memory consuming step. I was wondering if anyone could help me by guiding me about any possible remedy to declare input parameters of the pipeline as some global inputs and avoiding the pipeline to create input directory for each Task separately and coping and pasting the common inputs (such as unmapped Bam, and Bai files) for each task.

I have heard about a configuration option of Cromwell engine to use aliases , but I have no idea about how to do it.

Thanks

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  Tiffany Miller

  • January 27, 2020 22:49

  HI Naser Elmi you could try using a struct and importing it. Check out the spec here for details. An example of it being used on Terra (a platform our team supports) to do an exome analysis is here. See the import statement for the GermlineStructs.wdl

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