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rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements
BSD 3-Clause "New" or "Revised" License
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Replace POLCA with pypolca #135

Closed jmtsuji closed 5 months ago

jmtsuji commented 5 months ago

As discussed in #125 , pypolca was recently developed as a standalone replacement for POLCA. This PR implements pypolca in place of POLCA in rotary for increased stability and multi-OS support.

jmtsuji commented 5 months ago

@LeeBergstrand Mind giving your review on this PR to change POLCA to pypolca? Thanks!

LeeBergstrand commented 5 months ago

@jmtsuji Looks excellent so far. Just a few minor questions to address, and we should be able to merge it in promptly.

jmtsuji commented 5 months ago

@LeeBergstrand I left comments for you, including a reply about the temp() designation of output files. Let me know your thoughts -- thanks.

LeeBergstrand commented 5 months ago

@LeeBergstrand I left comments for you, including a reply about the temp() designation of output files. Let me know your thoughts -- thanks.

@jmtsuji Let's try adding temp to both rules. I don't remember trying to add temp to one or the other on purpose. I think I intended to add temp to both.

jmtsuji commented 5 months ago

@LeeBergstrand Everything seems to be resolved (see the comments above) -- let me know if you notice anything else or if you are OK to merge this PR. If you are OK, then feel free to go ahead and merge this into develop!

LeeBergstrand commented 5 months ago

Done!