Add snakemake workflow #1
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- bring environment up to date - add workflow infrastructure - adjust download script with path setting
- adjust paths - fix readme - add workflow components
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Brilliant - thanks for the improvements! Snakemake looks like a promising standard, conda unfix is great, and automatic creation of folders is convenient. I'm accepted your changes to: "remove the PROJECT_PATH, CACHE_PATH, OUT_PATH as do some os.path setting instead" for consistency, but I'm not convinced this is an improvement. I suspect python-dotenv may give more flexibility with only marginally higher overhead. I'd be keen to discuss and potentially lobby for python-dotenv. |
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@stephenjlee happy to learn more about the python-dotenv |
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@stephenjlee , First of all: COOL TOOL 馃挴. I added in this PR a first snakemake workflow to the package. This makes execution easy on local and cluster machines, and is useful if one wants to add more options, other workflows, or packages.
Further changes:
/outand/cachefoldersI am keeping this here as a Pull Request. Feel free to test it on my branch and request changes if necessary. This PR is also not urgent, we can talk about it at the next meeting.