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adapt modules for snakemake 8 #13
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All the libraries used across the current MR. PARETO Snakefiles:
It seems like the only one's that are not from the Python Standard Library are pandas, numpy and pyyaml. We should at least document the numpy and pandas dependencies. |
Let's find out which packages actually come with the minimal snakemake installation (the one that would create a problem because of missing packages). e.g., is yaml/pyaml for sure in there? then we could make one |
It is indeed:
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Additionally these are the numpy and pandas versions that come with the big snakemake8:
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I checked the RNA pipeline again and interestingly they only use the in all other rules they only use the Unsure what to do ie how to decouple resource specifications form workflow configuration meaningfully without adding complexity dor the enduser. |
To bump all modules to snakemake 8 (#12) we primarily need to document the libraries required to process the initial Snakemake file. These should be added to
envs/global.yaml
and cross-linked into the Snakemake file with aconda
directive. See 'global workflow dependencies' in the snakemake docs. We also need to check the documentation for each module such that it makes sense for Snakemake8.one-off (first in unsupervised_analysis)
envs/global.yaml
specifying required software for Snakefile executionconfig.yaml
for each module
partition
parameter fromparams
workflow/profiles/default/config.yaml
config/README.md
envs/global.yaml
to workflowconda
directive inSnakefile
for global specifications at the beginning of your workflow, before you import or use any of those additional packages8.20.1
Modules
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