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CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
https://www.cdc.gov/ncezid/divisions-offices/about-dhqp.html
Apache License 2.0
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Refactor failed summary handling #152

Open slsevilla opened 8 months ago

slsevilla commented 8 months ago

Description

I think we can improve the failed summary handling, but I'm not clear on what is the goal of the fetched_failed_summaries module, and since I don't have failed samples for SPADES I'm not able to see the full picture. Can you help me get an idea of what the goal is - I'd be happy to think through a new strategy for these since I THINK that this will trigger a restart of the pipeline upstream if there are failed samples.

jvhagey commented 5 months ago

I made some changes to how this is handled here https://github.com/CDCgov/phoenix/commit/e5ef2e526a16e29411252c81910c58dfbb2e16ca and here https://github.com/CDCgov/phoenix/commit/1f8c9e775ccc502a9e6ec650305ac5311fc44f92. Can you give it a try the v2.2.0-dev and see if the resume works correctly now?