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[FEATURE]Add .csi output to deepvariant/rundeepvariant module

Open yz533cb opened this issue 6 months ago • 0 comments

Is your feature request related to a problem? Please describe

Module rundeepvariant output channels include index-output, which currently supports .tbi format.

Deepvariant also supports .csi index output, when the size of any reference chromosomes exceed 512M: https://github.com/google/deepvariant/blob/r1.9/deepvariant/postprocess_variants.py#L1387-L1401

Would it be good to update the output channel of the nf-core module as well?

Describe the solution you'd like

The expected changes are reflected in this .diff file we currently use: https://github.com/sanger-tol/variantcalling/blob/dev/modules/nf-core/deepvariant/rundeepvariant/deepvariant-rundeepvariant.diff

yz533cb avatar Jun 23 '25 15:06 yz533cb