config.yml

## Input and output options ##
# this section is the minimum information that is required and must be stated
fasta_path: "<path/to/assembly.fasta>" # path to assembly FASTA
gff_path: "<path/to/assembly.gff>" # path to GFF
output_path: "<path/to/output_directory/>" # directory to save results to
taxon_id: "<NCBI taxon ID>" # NCBI Taxon ID of query species
bam_path_1: "<path/to/mapping.bam>" # path to BAM file; to add multiple duplicate the parameter and increase the number in the suffix

## Taxonomic assignment options ##
taxon_exclude: "TRUE" # exclude query taxon from taxonomic assignment [TRUE/FALSE]
assignment_mode: "exhaustive" # mode for taxonomic assignment [exhaustive/quick]; see Documentation for details

## PCA options ##
# gene descriptors to be used in the PCA; see Documentation for details on options
input_variables: "c_name,c_num_of_genes,c_len,c_genelenm,c_genelensd,g_len,g_lendev_c,g_abspos,g_terminal,c_cov,c_covsd,g_cov,g_covsd,g_covdev_c,c_pearson_r,g_pearson_r_o,g_pearson_r_c"

## Plot output options ##
update_plots: "FALSE" # only update the plots (use if you changed settings below) [TRUE/FALSE]
num_groups_plot: "25" # number of taxa to display in plot (taxa are automatically merged at higher ranks) [X/all]
merging_labels: [] # influence the merging of taxa; see Documentation for details on options