/*
 * -------------------------------------------------
 *  Nextflow config file for reference genome
 * -------------------------------------------------
 * These references have to be build manually due
 * to ERCC spike-ins.
 * Can be used by any config that customizes the base
 * path using $params.genomes_base / --genomes_base
 */

params {
    genomes {
        'GRCh38' {
            fasta        = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa"
            fai          = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa.fai"
            gtf          = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.gtf"
            chrgtf       = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.chr.gtf"
            transcript   = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.cdna.all.fa.gz"
            refflat      = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.chr.gtf.refflat"
            rrna_intervals= "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.interval_list"
        }
    }
}
