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jbloomlab / barcoded_flu_pdmH1N1

Barcoded pdmH1N1 virus hashing experiment
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tracking changes to code #57

Open jbloom opened 3 years ago

jbloom commented 3 years ago

I think Snakemake has a way to directly track code so we don't need to define Jupyter notebooks as input.

jbloom commented 3 years ago

This can be done using the --list-code-changes option. However, that option is currently broken due to a bug in snakemake. I have submitted a pull request to snakemake to fix that: https://github.com/snakemake/snakemake/pull/695

Once that pull request is merged into a new snakemake version, we can add the --list-code-changes option to a -R directive when running snakemake, and then eliminate the notebooks as inputs.

dbacsik commented 2 years ago

@jbloom Your snakemake PR was approved and merged. Does this seem like an important issue to address? If so, I am happy to refactor the rules. If not, I am fine leaving the rules as they are.