params.config

params {
	
	// Input options
	// mandatory
	tsv 				= "$projectDir/data/assemblies.tsv" 	// we could change this to NULL
	column_id_value 	= "Assembly Accession"
	column_path_value 	= "Path"
	column_taxid_value 	= "Organism Taxonomic ID"


	// General options
	// optional
	outdir	= "$projectDir/output"


    // GeneidX parameters
  	parameter_path      = "$projectDir/data/Parameter_files.taxid/"

	use_masking 		= false
	store_param_files 	= false
	assemblies_dir 		= ""

    // Protein query configuration
	uniref_identity 	= 0.9
	proteins_lower_lim 	= 90000
  	proteins_upper_lim 	= 130000


	// Parameter file parameters
	auto_params_selection_files_path 	= "https://raw.githubusercontent.com/guigolab/geneid-parameter-files/main/parameter_files"
	auto_params_selection_matrix_path 	= "https://raw.githubusercontent.com/guigolab/geneid-parameter-files/main/matrix.tsv"

	maps_param_values = [ 
		"no_score"		: -0.10
	]


	general_gene_params = "$projectDir/data/general_gene_model.param"

	match_score_min 	= 300
	match_ORF_min 		= 100

	intron_margin 		= 40

	min_intron_size 	= 20
	max_intron_size 	= 10000

	source_uniprot		= 1

    min_contig_size     = 5000
    npart_size          = 200000
    // npart_size          = 200000000


	// RepeatMasker part of the parameters

    // RepeatMasker options
    rm_species           	= null 	// this one could be removed
    rm_lib               	= null 	// this one could be removed

    // place to store the repeat files
    repeats_data_path   	= "$projectDir/data"

    // update repeat prot file
    update_repeat_prot_file	= 0
    
    // Do not remove it, required by RepeatMasker
    dummy_gff            	= 'assets/empty.gff3'


}