CDCgov / phoenix

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

Apache License 2.0

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Create flags to turn on/off modules #153

Closed slsevilla closed 1 month ago

slsevilla commented 3 months ago

Description

Expand flags in the nextflow.config to allow user control over which pipeline components are run

slsevilla commented 3 months ago

flags include:

busco: 320cb64f1e824d5a7672fc513e13935af3ec9075
ncbi_excel_creation: 47a0c5cf91ab185d2e40b990dcd676371cb2fe4b
extended_qc: 47a0c5cf91ab185d2e40b990dcd676371cb2fe4b
run_srst2_mlst: a338622
run_griphin: a338622

jvhagey commented 1 month ago

If folks want to run BUSCO and/or SRST2 they can use the CDC_PHOENIX entry point. Griphin is a summary file so I don't see the value of turning that on/off. ncbi_excel_creation already has a flag to turn it on or off the default is to have it off. Granted the flag for this is a bit confusing because I have a layer of control that force it to be false if its not CDC_PHOENIX or the PHOENIX entry.