To-do before paper submission

AlexanderLabWHOI / EUKulele

Automatic eukaryotic taxonomic classification

MIT License

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To-do before paper submission #3

Closed halexand closed 2 years ago

halexand commented 4 years ago

[x] Add license.
[ ] Codify flow diagram.
[x] Add BUSCO assessment for metaT and metaG
[x] Move away from config.yaml and towards commandline input. One issue I see here is how to deal with the cluster config file. I feel that it is easiest just to keep it as is. How to we use submit-script.sh with commandline ops?

akrinos commented 4 years ago

Remodeling branch now has a fully Python-based option, in which there is a file, EUKulele-config.py, that will parse the command-line flags from the config.yaml file if you wish. Otherwise, everything can be specified as flags. This also resolves the issues with the cluster.yaml file, because the SLURM options only need to be specified once for the entire run.

akrinos commented 4 years ago

Akrinos branch demonstrates the BUSCO assessment workflow for one sample organism for the METs. I need to think more about how to do it for the MAGs, because it will require more design on my part. Currently, I am using my outputs from taxonomy estimation and visualization for the BUSCO process. In the new workflow in the remodeling branch, users may specify as many organisms/classes/etc. as they wish in either a provided file, a space-separated list as command-line inputs, or a tab-delimited file (need the names of the organisms at whatever taxonomic level you're interested in, then what that taxonomic level is).