Write regions file as VCF is being processed instead of saving in memory

wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL

MIT License

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Write regions file as VCF is being processed instead of saving in memory #159

Open susannasiebert opened 2 months ago

susannasiebert commented 2 months ago

Closes https://github.com/genome/docker-bam_readcount_helper-cwl/issues/7

I tried running this step with the miniwdl helper locally but have been running into issues getting miniwdl to work. This change should be independently tested before merging.

susannasiebert commented 1 month ago

Kartik ran the updated wdl on some test data and it complete successfully. The output looks sane to me.