/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file for iGenomes paths
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Defines reference genomes using iGenome paths.
    Can be used by any config that customises the base path using:
        $params.igenomes_base / --igenomes_base
----------------------------------------------------------------------------------------
*/

params {
    // illumina iGenomes reference file paths
    genomes {
        'GATK.GRCh37' {
            ascat_alleles         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_alleles_hg19.zip"
            ascat_genome          = 'hg19'
            ascat_loci            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_loci_hg19.zip"
            ascat_loci_gc         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/GC_G1000_hg19.zip"
            ascat_loci_rt         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/RT_G1000_hg19.zip"
            bwa                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/"
            chr_dir               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes"
            dbsnp                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.gz"
            dbsnp_tbi             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.gz.tbi"
            dbsnp_vqsr            = '--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_138.b37.vcf.gz'
            dict                  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
            fasta                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
            fasta_fai             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai"
            germline_resource     = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz"
            germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz.tbi"
            intervals             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list"
            known_snps            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz"
            known_snps_tbi        = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi"
            known_snps_vqsr       = '--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_phase1.snps.high_confidence.b37.vcf.gz'
            known_indels          = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz"
            known_indels_tbi      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz.tbi"
            known_indels_vqsr     = '--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_phase1.indels.b37.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.b37.vcf.gz'
            mappability           = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
            snpeff_db             = 'GRCh37.87'
            snpeff_genome         = 'GRCh37'
            snpeff_version        = '5.1'
            vep_cache_version     = 106
            vep_genome            = 'GRCh37'
            vep_species           = 'homo_sapiens'
            vep_version           = '106.1'
        }
        'GATK.GRCh38' {
            ascat_alleles         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip"
            ascat_genome          = 'hg38'
            ascat_loci            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip"
            ascat_loci_gc         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip"
            ascat_loci_rt         = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip"
            bwa                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/"
            bwamem2               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/"
            dragmap               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/"
            chr_dir               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes"
            dbsnp                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
            dbsnp_tbi             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
            dbsnp_vqsr            = '--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz'
            dict                  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
            fasta                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
            fasta_fai             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
            germline_resource     = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz"
            germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi"
            intervals             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions.hg38.bed"
            known_snps            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz"
            known_snps_tbi        = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi"
            known_snps_vqsr       = '--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz'
            known_indels          = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
            known_indels_tbi      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
            known_indels_vqsr     = '--resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
            mappability           = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem"
            pon                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz"
            pon_tbi               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
            snpeff_db             = 'GRCh38.105'
            snpeff_genome         = 'GRCh38'
            snpeff_version        = '5.1'
            vep_cache_version     = 106
            vep_genome            = 'GRCh38'
            vep_species           = 'homo_sapiens'
            vep_version           = '106.1'
        }
        'Ensembl.GRCh37' {
            bwa                   = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
            snpeff_db             = 'GRCh37.87'
            snpeff_genome         = 'GRCh37'
            snpeff_version        = '5.1'
            vep_cache_version     = 106
            vep_genome            = 'GRCh37'
            vep_species           = 'homo_sapiens'
            vep_version           = '106.1'
        }
        'NCBI.GRCh38' {
            bwa                   = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
            snpeff_db             = 'GRCh38.105'
            snpeff_genome         = 'GRCh38'
            snpeff_version        = '5.1'
            vep_cache_version     = 106
            vep_genome            = 'GRCh38'
            vep_species           = 'homo_sapiens'
            vep_version           = '106.1'
        }
        'GRCm38' {
            bwa                   = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
            chr_dir               = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes"
            dbsnp                 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
            dbsnp_tbi             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
            dict                  = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.dict"
            fasta                 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
            fasta_fai             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai"
            intervals             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/intervals/GRCm38_calling_list.bed"
            known_indels          = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
            known_indels_tbi      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
            mappability           = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem"
            readme                = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
            snpeff_db             = 'GRCm38.99'
            snpeff_genome         = 'GRCm38'
            snpeff_version        = '5.1'
            vep_cache_version     = 102
            vep_genome            = 'GRCm38'
            vep_species           = 'mus_musculus'
            vep_version           = '106.1'
        }
        'TAIR10' {
            bwa                   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
        }
        'EB2' {
            bwa                   = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
        }
        'UMD3.1' {
            bwa                   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
        }
        'WBcel235' {
            bwa                   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
            snpeff_db             = 'WBcel235.105'
            snpeff_genome         = 'WBcel235'
            snpeff_version        = '5.1'
            vep_cache_version     = 106
            vep_genome            = 'WBcel235'
            vep_species           = 'caenorhabditis_elegans'
            vep_version           = '106.1'
        }
        'CanFam3.1' {
            bwa                   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
            snpeff_db             = 'CanFam3.1.99'
            snpeff_genome         = 'CanFam3.1'
            snpeff_version        = '5.1'
            vep_cache_version     = 104
            vep_genome            = 'CanFam3.1'
            vep_species           = 'canis_lupus_familiaris'
            vep_version           = '106.1'
        }
        'GRCz10' {
            bwa                   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
        }
        'BDGP6' {
            bwa                   = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
        }
        'EquCab2' {
            bwa                   = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
        }
        'EB1' {
            bwa                   = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
        }
        'Galgal4' {
            bwa                   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
        }
        'Gm01' {
            bwa                   = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
        }
        'Mmul_1' {
            bwa                   = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
        }
        'IRGSP-1.0' {
            bwa                   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
        }
        'CHIMP2.1.4' {
            bwa                   = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
        }
        'Rnor_5.0' {
            bwa                   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
        }
        'Rnor_6.0' {
            bwa                   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
        }
        'R64-1-1' {
            bwa                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
        }
        'EF2' {
            bwa                   = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
        }
        'Sbi1' {
            bwa                   = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
        }
        'Sscrofa10.2' {
            bwa                   = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
        }
        'AGPv3' {
            bwa                   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
        }
        'hg38' {
            bwa                   = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
        }
        'hg19' {
            bwa                   = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
        }
        'mm10' {
            bwa                   = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
        }
        'bosTau8' {
            bwa                   = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
        }
        'ce10' {
            bwa                   = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
        }
        'canFam3' {
            bwa                   = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
        }
        'danRer10' {
            bwa                   = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
        }
        'dm6' {
            bwa                   = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
        }
        'equCab2' {
            bwa                   = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
        }
        'galGal4' {
            bwa                   = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
        }
        'panTro4' {
            bwa                   = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
        }
        'rn6' {
            bwa                   = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
        }
        'sacCer3' {
            bwa                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
        }
        'susScr3' {
            bwa                   = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
            fasta                 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
            readme                = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
        }
    }
}
