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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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export variant file (vcf) #232

Closed oliverdrechsel closed 2 years ago

oliverdrechsel commented 2 years ago

Is your feature request related to a problem? Please describe. Currently, the called variants are not exported to the results folder and are hidden in work folder.

Describe the solution you'd like https://github.com/replikation/poreCov/blob/master/workflows/process/artic.nf may be modified to publish as well SNP_${name}.pass.vcf

Describe alternatives you've considered none

Additional context work folder tends to be quite bulky, hence we remove them soon after porecov is finished

hoelzer commented 2 years ago

Yes, I support that. The VCF is kinda often needed for some downstream stuff. And maybe we will also add some additional visualization soon where it would be anyway good to also provide the VCF for further checks.