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nextstrain / ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
MIT License
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Remove `--stats` when we upgrade to Snakemake v8 #452

Open joverlee521 opened 3 months ago

joverlee521 commented 3 months ago

Follow up to https://github.com/nextstrain/ncov-ingest/pull/451.

We are using the Snakemake --stats flag to get workflow stats for GISAID and GenBank ingest to help with #446. If/when we ever upgrade Snakemake to v8, the --stats flag is no longer supported and will need to be removed.

Upgrading Snakemake is dependent on updating the nextstrain docker-base image and then running the update-image workflow in this repo since the workflows are using the nextstrain/ncov-ingest Docker image.

Alternatively, we can pin Snakemake <8 in this repo, but we can make that decision later.

corneliusroemer commented 1 month ago

I don't see why we shouldn't support snakemake 8. I think it's bad we get stuck at old versions and can't use new features.

It's good that we are updating now but I agree that pinning should be easy workaround in case we don't have time to change the worklow immediately