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merenlab / merenlab.org

Web content for Meren Lab
http://merenlab.org
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Reproducible workflow for Veseli et al 2023 #149

Closed ivagljiva closed 1 year ago

ivagljiva commented 1 year ago

This PR adds the reproducible workflow for my upcoming paper. I have tested the code within to the best of my ability (considering I don't have the time or computational capacity to download all the data and re-run all the snakemake workflows).

There are still two things that need to be added to this webpage.

1) the Zenodo link to the datapack for the 408 gut metagenome assemblies. I tried many times, but I couldn't upload that huge datapack to the server with my current internet situation. I will upload it once I return to Chicago and add the links afterwards (they are all marked with FIXMEs).

2) Statistical code from Yiqun. Once he sends those to me, I will update the page, and potentially make a new version of the datapack including his code (we'll see). There is a notice in the relevant section of the page indicating that this code will be added later.

Regardless, I'm going to merge this immediately.

meren commented 1 year ago

Excellent documentation and reproducible workflow, Iva! You even uploaded the contigs-dbs for GTDB genomes :') Thank you for doing this.