/*
 * -------------------------------------------------
 *  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 {
    'GRCh37' {
      ac_loci                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci"
      ac_loci_gc              = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
      bwa                     = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
      chr_dir                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes"
      chr_length              = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Length/human_g1k_v37_decoy.len"
      dbsnp                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf"
      dbsnp_index             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx"
      dict                    = "${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       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz"
      germline_resource_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz.tbi"
      intervals               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list"
      known_indels            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
      known_indels_index      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
      mappability             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
      snpeff_db               = 'GRCh37.75'
      species                 = 'homo_sapiens'
      vep_cache_version       = '99'
    }
    'Ensembl.GRCh37' {
      fasta                   = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
      bwa                     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa"
    }
    'GRCh38' {
      ac_loci                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci"
      ac_loci_gc              = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc"
      bwa                     = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
      chr_dir                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes"
      chr_length              = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len"
      dbsnp                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
      dbsnp_index             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
      dict                    = "${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       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz"
      germline_resource_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz.tbi"
      intervals               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions.hg38.bed"
      known_indels            = "${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_index      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
      mappability             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem"
      snpeff_db               = 'GRCh38.86'
      species                 = 'homo_sapiens'
      vep_cache_version       = '99'
    }
    'NCBI.GRCh38' {
      fasta                   = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
      bwa                     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa"
    }
    'GRCm38' {
      bwa                     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      chr_dir                 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes"
      chr_length              = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Length/GRCm38.len"
      dbsnp                   = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
      dbsnp_index             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
      dict                    = "${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_index      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
      mappability             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem"
      snpeff_db               = 'GRCm38.86'
      species                 = 'mus_musculus'
      vep_cache_version       = '99'
    }
    'TAIR10' {
      bwa                     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
    }
    'EB2' {
      bwa                     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
    }
    'UMD3.1' {
      bwa                     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
    }
    'bosTau8' {
      bwa                     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
    }
    'WBcel235' {
      bwa                     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
      snpeff_db               = 'WBcel235.86'
      species                 = 'caenorhabditis_elegans'
      vep_cache_version       = '99'
    }
    'ce10' {
      bwa                     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
    }
    'CanFam3.1' {
      bwa                     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
    }
    'canFam3' {
      bwa                     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
    }
    'GRCz10' {
      bwa                     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
    }
    'danRer10' {
      bwa                     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
    }
    'BDGP6' {
      bwa                     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
    }
    'dm6' {
      bwa                     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
    }
    'EquCab2' {
      bwa                     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
    }
    'equCab2' {
      bwa                     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
    }
    'EB1' {
      bwa                     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
    }
    'Galgal4' {
      bwa                     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
    }
    'galGal4' {
      bwa                     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
    }
    'Gm01' {
      bwa                     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
    }
    'hg38' {
      bwa                     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
    }
    'hg19' {
      bwa                     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
    }
    'Mmul_1' {
      bwa                     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
    }
    'mm10' {
      bwa                     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
    }
    'IRGSP-1.0' {
      bwa                     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
    }
    'CHIMP2.1.4' {
      bwa                     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
    }
    'panTro4' {
      bwa                     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
    }
    'Rnor_6.0' {
      bwa                     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
    }
    'rn6' {
      bwa                     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
    }
    'R64-1-1' {
      bwa                     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
    }
    'sacCer3' {
      bwa                     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
    }
    'EF2' {
      bwa                     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
    }
    'Sbi1' {
      bwa                     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
    }
    'Sscrofa10.2' {
      bwa                     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
    }
    'susScr3' {
      bwa                     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
    }
    'AGPv3' {
      bwa                     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
      fasta                   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
    }
  }
}
