MAMBA.params.yaml

#----------------------------------------#
#                                        #
#     PIPELINE GLOBAL PARAMS             #
#                                        #
#----------------------------------------#
metasheet: meta.csv

#------       Memory params in MegaBytes (MB)  -----------#
min_mem: 5000    #5G
med_mem: 15000   #15G
max_mem: 30000   #30G


#------               Parallelization          -----------#
min_cores: 1   #this is always 1 by default
med_cores: 8   #except raxml all other multi core modules use this many threads 
max_cores: 12  #only raxml uses maximum cores 


#------ VCF Filtering Based On ReadDepth & Map Quality ---#
read_depth: 
map_quality:

#----------------------------------------#
#                                        #
#   Core Genome Based Approach - Params  #
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#----------------------------------------#

#------                prokka params           -----------#
kingdom:                    #possible values are [Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria')]
genus: Staphylococcus       #(default 'Genus')
species: aureus             #(default 'species')
strain:                     #(default 'strain')
#------- NOTE: Currently, gram option is not supported due to licensing issues with SignalP software ---------#
gram:                       #possible values are [neg|pos (default '')]


#------                 GATK params            -----------#
#GATK Executable - Due to licensing issues, user has to provide the executable 'only if' gatk is not already in PATH
gatk_exec:



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#  Reference Based Approach - Params     #
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#----------------------------------------#

reference:                  #/path/to/reference-genome.fasta