/*
 * -------------------------------------------------
 *  Nextflow config file for Genomes paths
 * -------------------------------------------------
 * Defines reference genomes
 * Can be used by any config that customises the base
 * path using $params.genomes_base / --genomes_base
 */

params {
       bwt2_index = '/data/annotations/pipelines/Human/hg19/indexes/bowtie2/hg19'
       bwt2_opts_end2end = '--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'
       bwt2_opts_trimmed = '--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder'
       restriction_fragment_bed = '/data/users/nservant/Apps/HiC-Pro_annotation/HindIII_resfrag_hg19.bed'
       chromosome_size = '/data/users/nservant/Apps/HiC-Pro_annotation/chrom_hg19.sizes'
}