Create flags to turn on/off modules

[slsevilla]

Description

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

[slsevilla]

flags include:

• busco: 320cb64
• ncbi_excel_creation: 47a0c5c
• extended_qc: 47a0c5c
• run_srst2_mlst: a338622
• run_griphin: a338622

[jvhagey]

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.