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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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Add samtools faidx sequence retrieval #80

Closed percyfal closed 1 year ago

percyfal commented 1 year ago

Fixes #58

percyfal commented 1 year ago

@clami66 @LeandroRitter I added a samtools faidx step and modified the Breadth_Of_Coverage rule accordingly. To ensure the indexing step runs, Breadth_Of_Coverage has to include the index file as its input. For some reason, we have throughout the workflow never used the malt database as an input but rather as a parameter. I can't remember if we had any explicit reason to not use it as an input? Fear of accidentally deleting it through snakemake in some way?

clami66 commented 1 year ago

LGTM!