CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
Apache License 2.0
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convert --coverage to integer to avoid issues on Seqera Cloud #172

Closed DOH-JDJ0303 closed 3 months ago

DOH-JDJ0303 commented 3 months ago

Minor change to address issue faced when running PHoeNIx on Seqera Cloud. Seqera Cloud seems to change the --coverage parameter value to a string, regardless of if you supply it as an integer in the config file. I was not able to replicate this on command line, but I have confirmed that this simple change fixes the problem on Seqera Cloud.