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: subworkflow for isolate genomes #127

Open franciscozorrilla opened 1 year ago

franciscozorrilla commented 1 year ago

🦠 Isolate genomes subworkflow 🔦

Adding support for isolate genome assembly in the next version of metaGEM 💎

🐍 Snakefile tasks

[x] create shovill rule for dealing with isolate assembly data
[x] create dRep rule for derelplicating megahit assembly, metaGEM-reassembled bin, and shovill output to select best genome
[ ] create helper rule to populate drep input from corresponding input subfolders

🔨 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: add new perl environment for shovill (to also include prokka, roary, etc.), dRep could go in main metaGEM env
[ ] conda recipe: update
[ ] main readme file: text and eventually figure