search

Arcadia-Science / prehgt

A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT
MIT License
12 stars 6 forks source link

Update Snakemake to parity with Nextflow #55

Closed lebovic closed 11 months ago

lebovic commented 11 months ago

Hey all! This (roughly) brings Snakemake to parity with Nextflow.

Changes:

  1. Adds resource specs for parallelization (mimicking the Nextflow resource requests)
  2. Fixes the checkpoint_download_reference_genomes globbing

I tested these changes on our distributed infrastructure, but not on a single instance. I'm not sure if it's desired to include large resource requests for local runs (e.g. 200 GB of RAM for compositional_scans_to_hgt_candidates), but it looks like that's similar to what's happening on the Nextflow side.