Immuno workflow annotated VCF gets written as a .vcf file instead of .vcf.gz

wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL

MIT License

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Immuno workflow annotated VCF gets written as a .vcf file instead of .vcf.gz #126

Closed susannasiebert closed 1 year ago

malachig commented 1 year ago

It does? Can you add more detail?

When I pull results down, the final VCF I have been looking at is annotated.expression.vcf.gz

susannasiebert commented 1 year ago

I think this might be an oddity from downloading through the cloud console web interface.

tmooney commented 1 year ago

I did get a .gz ending when I went to the data tab of the immuno run and copied the gs:// path for pvacseq_annotated_expression_vcf_gz to use gsutil cp. But yeah, when I click the link in the datatable Terra "helpfully" renames the file to be downloaded to not end in .gz... I guess this is more an issue specifically with terra than with the WDL per se.

susannasiebert commented 1 year ago

yeah, I think this issue can be closed.