CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens

Apache License 2.0

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handle flags in nextflow.config rather than in main/modules #150

Closed slsevilla closed 1 month ago

slsevilla commented 4 months ago

Description

move flags from within main.nf / phoneix.nf to config to improve reproducibility and documentation

slsevilla commented 4 months ago

create busco with commit 320cb64f1e824d5a7672fc513e13935af3ec9075

jvhagey commented 1 month ago

If people want to run BUSCO they can just use the entry CDC_PHOENIX. Not sure what the utility of adding additional flags would be, I am trying to keep this not complicated for non-power users. Reopen if there is more interest in this.