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PacificBiosciences / pb-human-wgs-workflow-snakemake

DEPRECATED - Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
BSD 3-Clause Clear License
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Updating plof file #136

Closed lauragails closed 1 year ago

lauragails commented 1 year ago

Hello, I was double-checking the config.yaml file and I think the lof_lookup_url is out of date. Haven't gotten to where this is used, but writing issue now for future troubleshooting.

From gnomad link is: https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz

Source: https://gnomad.broadinstitute.org/downloads

In config.yaml: lof_lookup_url: 'https://storage.googleapis.com/gnomad-public/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz'

Thank you, and I hope you had a happy Thanksgiving!

williamrowell commented 1 year ago

We tend to just download the entire resources directory instead of depend on these rules, so the rules have gone untested for a while. I think the solution here is that we'll remove these rules and you can get these files directly from us. Send an email and I'll point you to the ftp with the full reference and resources directories.

lauragails commented 1 year ago

Gotcha - I have those directories already from other coorespondance with PacBio, so I think we can close the ticket!