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iqbal-lab-org / pling

Plasmid analysis using rearrangement distances
MIT License
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Plasnet integration PR series (3/n): refactor: refactor common rules and functions from workflows into common_rules.smk #35

Closed leoisl closed 7 months ago

leoisl commented 7 months ago

This PR contains some refactors preparing for the main plasnet integration PR.

It refactors 2 rules (create_genomes_tsv and cat_jaccard) and 2 functions (get_pairs() and get_files()) that were duplicated between two workflows (pling/align_snakemake/Snakefile and pling/jac_network_snakemake/Snakefile) into a single snakemake file (pling/common_rules/common_rules.smk) which is now included in both workflows.

Sorry that rule create_genomes_tsv was not introduced before, it is a new rule required to integrate plasnet into pling.