A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hello everyone!

I’m exploring `--vep_loftee`, but I’m unsure how to supply LOFTEE’s support files.

In the <https://github.com/nf-core/sarek/blob/b97952e5bac68d5deb93d4a3349a45f146be9830/conf/modules/annotate.config#L32-L45|Sarek revision we use>, `--vep_loftee` adds the LoF plugin argument. I can see <https://github.com/nf-core/sarek/blob/b97952e5bac68d5deb93d4a3349a45f146be9830/main.nf#L207-L231|staging for other VEP plugin files>, but I haven’t found equivalent LOFTEE file parameters.

Is there an existing supported way to place these files in the VEP cache and pass their paths to LOFTEE? If not, would an upstream PR adding LOFTEE file parameters, staging, and validation be welcome?

PRs are always welcome, I might have missed the extra files when adding this plugin

See what you think <@UE6D8290F> <https://github.com/nf-core/sarek/pull/2301|github.com/nf-core/sarek/pull/2301>

Thanks for the review <@UE6D8290F>! Pushed some fixes