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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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export filtering step to standalone script #89

Closed clami66 closed 1 year ago

clami66 commented 1 year ago

Here the krakenuniq output filtering is done only once in a small script, then the krakenuniq.output.filtered output is used wherever possible to avoid redundant filtering steps

Notice how the hardcoded 1000 in filtered_taxIDs_kmers1000 should be changed at a later stage since the "1000" comes from a configurable parameter

clami66 commented 1 year ago

Fixes #88

clami66 commented 1 year ago

And here is how the DAG looks now: image

clami66 commented 1 year ago

It is for the test output. Should we add a diff check in the github actions?

percyfal commented 1 year ago

I guess at some point we should. It's one thing that the workflow runs, another that we actually can reproduce the same results. I think this will take some time to implement though. Anyhow, I'll go ahead and merge and we could keep this in mind for the future.