franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

https://franciscozorrilla.github.io/metaGEM/

MIT License

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feature: add support for eggnog-mapper #129

Open franciscozorrilla opened 1 year ago

franciscozorrilla commented 1 year ago

🥚 eggNOG-mapper for better functional annotation 🍸

🐍 Snakefile tasks

[x] create eggnog-mapper rule for processing ORF-annotated protein fasta files of genomes
[ ] create helper/supplementary rule to deal with large number of genomes (e.g. per sample submission of jobs)

🔨 Additional modifications for full integration/support

[ ] metaGEM.sh: add options + support for new tasks
[ ] config.yaml: add params used in new tasks
[ ] config readme file: eggnog-mapper could go in main metaGEM env
[ ] conda recipe: update
[ ] main readme file: text and eventually figure