/* groovylint-disable DuplicateNumberLiteral, DuplicateStringLiteral */
singularity.enabled = true
singularity.cacheDir = "/pi/ozkan.aydemir-umw/share/containers/nfcore/"
singularity.libraryDir = "/pi/ozkan.aydemir-umw/share/containers/"
singularity.runOptions = '-B /share,/pi,/home'

executor.exitReadTimeout = '5 min'
executor.perJobMemLimit = false
executor.perTaskReserve = true

params.DOWNDIR = (params.DOWNDIR) ? params.DOWNDIR : ""

// Export these variables to prevent local Python/R libraries from conflicting
// with those in the container

env {
  PYTHONNOUSERSITE = 1
  R_PROFILE_USER = "/opt/.Rprofile"
  R_ENVIRON_USER = "/opt/.Renviron"
}

/* groovylint-disable Indentation, LineLength */
/* groovylint-disable CouldBeSwitchStatement, UnnecessaryObjectReferences */
params.genome_build = "" //* @dropdown @options:"human_hg38_gencode_v43_primary_comprehensive, human_hg38_gencode_v43_chromosomes_basic, human_hg38_HIV_JL_gencode_v43_chromosomes_basic, human_hg38_gencode_v43_k17_chromosomes_basic, human_hg19_gencode_v19_chromosomes_comprehensive, human_h38_mouse_mm10_chromosomes_basic, mouse_mm10_gencode_m25_primary_comprehensive, mouse_mm10_gencode_m25_chromosomes_basic, t_muris_PRJEB126_WBPS16, a_ceylanicum_PRJNA231479_WBPS16, custom"

_species = ""
_assembly = ""
_assembly_version = ""
_annotation = ""
_annotation_version = ""
params.g_build = ""
params.orgdb = ""
params.gprofiler_name = ""
params.ensembl_version = ""

//* autofill
if (params.genome_build == "human_hg38_gencode_v43_primary_comprehensive") {
    _species = "human"
    _assembly = "hg38"
    _assembly_version = "primary"
    _annotation = "gencode_v43"
    _annotation_version = "primary_comprehensive"
    params.g_build = "hg38"
    params.orgdb = "org.Hs.eg.db"
    params.gprofiler_name = "hsapiens"
    params.ensembl_version = 109
    params.ensembldb_id = "AH109606"
    params.mito_name = "chrM"
    params.genomesize = 2913022398
    params.common_name = "human"

} else if (params.genome_build == "human_hg38_gencode_v43_chromosomes_basic") {
    _species = "human"
    _assembly = "hg38"
    _assembly_version = "primary"
    _annotation = "gencode_v43"
    _annotation_version = "chromosomes_basic"
    params.g_build = "hg38"
    params.orgdb = "org.Hs.eg.db"
    params.gprofiler_name = "hsapiens"
    params.ensembl_version = 109
    params.ensembldb_id = "AH109606"
    params.mito_name = "chrM"
    params.genomesize = 2913022398
    params.common_name = "human"

} else if (params.genome_build == "human_hg38_HIV_JL_gencode_v43_chromosomes_basic") {
    _species = "human"
    _assembly = "hg38_HIV_JL"
    _assembly_version = "primary"
    _annotation = "gencode_v43"
    _annotation_version = "chromosomes_basic"
    params.g_build = "hg38"
    params.orgdb = "org.Hs.eg.db"
    params.gprofiler_name = "hsapiens"
    params.ensembl_version = 109
    params.ensembldb_id = "AH109606"
    params.mito_name = "chrM"
    params.genomesize = 2913022398
    params.common_name = "human"

}  else if (params.genome_build == "human_hg38_gencode_v43_k17_chromosomes_basic") {
    _species = "human"
    _assembly = "hg38"
    _assembly_version = "primary"
    _annotation = "gencode_v43"
    _annotation_version = "chromosomes_basic_k17"
    params.g_build = "hg38"
    params.orgdb = "org.Hs.eg.db"
    params.gprofiler_name = "hsapiens"
    params.ensembl_version = 109
    params.ensembldb_id = "AH109606"
    params.mito_name = "chrM"
    params.genomesize = 2913022398
    params.common_name = "human"

} else if (params.genome_build == "human_hg19_gencode_v19_chromosomes_comprehensive") {
    _species = "human"
    _assembly = "hg19"
    _assembly_version = "primary"
    _annotation = "gencode_v19"
    _annotation_version = "chromosomes_comprehensive"
    params.g_build = "hg19"
    params.orgdb = "org.Hs.eg.db"
    params.gprofiler_name = "hsapiens"
    params.ensembl_version = 74
    params.ensembldb_id = "NA"
    params.mito_name = "chrM"
    params.genomesize = 2864785220
    params.common_name = "human"

} else if (params.genome_build == "human_h38_mouse_mm10_chromosomes_basic") {
    _species = "human_mouse"
    _assembly = "hg38_mm10"
    _assembly_version = "primary"
    _annotation = "gencode_v43_m25"
    _annotation_version = "chromosomes_basic"
    params.g_build = "NA"
    params.orgdb = "NA"
    params.gprofiler_name = "NA"
    params.ensembl_version = "NA"

} else if (params.genome_build == "mouse_mm10_gencode_m25_primary_comprehensive") {
    _species = "mouse"
    _assembly = "mm10"
    _assembly_version = "primary"
    _annotation = "gencode_m25"
    _annotation_version = "primary_comprehensive"
    params.g_build = "mm10"
    params.orgdb = "org.Mm.eg.db"
    params.gprofiler_name = "mmusculus"
    params.ensembl_version = 100
    params.ensembldb_id = "AH79718"
    params.mito_name = "chrM"
    params.genomesize = 2652783500
    params.common_name = "mouse"

} else if (params.genome_build == "mouse_mm10_gencode_m25_chromosomes_basic") {
    _species = "mouse"
    _assembly = "mm10"
    _assembly_version = "primary"
    _annotation = "gencode_m25"
    _annotation_version = "chromosomes_basic"
    params.g_build = "mm10"
    params.orgdb = "org.Mm.eg.db"
    params.gprofiler_name = "mmusculus"
    params.ensembl_version = 100
    params.ensembldb_id = "AH79718"
    params.mito_name = "chrM"
    params.genomesize = 2652783500
    params.common_name = "mouse"

} else if (params.genome_build == "mouse_mm39_gencode_m36_chromosomes_basic") {
    _species = "mouse"
    _assembly = "mm39"
    _assembly_version = "primary"
    _annotation = "gencode_m36"
    _annotation_version = "chromosomes_basic"
    params.g_build = "mm39"
    params.orgdb = "org.Mm.eg.db"
    params.gprofiler_name = "mmusculus"
    params.ensembl_version = 113
    params.ensembldb_id = "AH119358"
    params.mito_name = "chrM"
    params.genomesize = 2654621783
    params.common_name = "mouse"

} else if (params.genome_build == "t_muris_PRJEB126_WBPS16") {
    _species = "t_muris"
    _assembly = "PRJEB126"
    _assembly_version = "main"
    _annotation = "WBPS16"
    _annotation_version = "main"
    params.g_build = "NA"
    params.orgdb = "NA"
    params.gprofiler_name = "tmuris"
    params.ensembl_version = "NA"

} else if (params.genome_build == "a_ceylanicum_PRJNA231479_WBPS16") {
    _species = "a_ceylanicum"
    _assembly = "PRJNA231479"
    _assembly_version = "main"
    _annotation = "WBPS16"
    _annotation_version = "main"
    params.g_build = "NA"
    params.orgdb = "NA"
    params.ensembl_version = "NA"
    params.gprofiler_name = "anceylprjna231479"
    params.ensembl_version = "NA"

} else if (params.genome_build == "custom") {
    params.genome       = "NA"
    params.genome_sizes = "NA"
    params.bed          = "NA"
    params.gtf          = "NA"
    params.transcripts  = "NA"

    params.star_index      = "NA"
    params.salmon_index  = "NA"
    params.bowtie2_index = "NA"
    params.bwa_index = "NA"

    params.commondb     = "NA"
    params.bowtieInd_rRNA  = "NA"
    params.bowtieInd_ercc  = "NA"
    params.bowtieInd_miRNA = "NA"
    params.bowtieInd_tRNA  = "NA"
    params.bowtieInd_piRNA = "NA"
    params.bowtieInd_snRNA = "NA"
    params.bowtieInd_rmsk  = "NA"

    params.apa_utr = "NA"
    params.apa_intron = "NA"
    params.apa_last_exon = "NA"
}

_share = ""
_genome_base = ""
$DEFAULT_IMAGE = ""
$SINGULARITY_IMAGE = ""

if ($HOSTNAME == "hpc.umassmed.edu") {
    _share = "/share/data/umw_biocore/dnext_data/genome_data"
    _genome_base = "/pi/ozkan.aydemir-umw/share/genomes"
    $DEFAULT_IMAGE = "singularity"
    $SINGULARITY_IMAGE = "quay.io/viascientific/rnaseq:4.0"
    $EXEC_OPTIONS = "-B /share,/pi,/home"
}

if (params.genome_build && $HOSTNAME) {
    /* groovylint-disable-next-line LineLength */
    params.genome_source   = "https://galaxyweb.umassmed.edu/pub/dnext_data/genome_data/${_species}/${_assembly}/main/genome.fa"
    /* groovylint-disable-next-line LineLength */
    params.gtf_source      = "https://galaxyweb.umassmed.edu/pub/dnext_data/genome_data/${_species}/${_assembly}/${_annotation}/genes/genes.gtf"
    params.commondb_source = "https://galaxyweb.umassmed.edu/pub/dnext_data/genome_data/${_species}/${_assembly}/commondb/"

    params.genome       = "${_genome_base}/${_species}/${_assembly}/${_assembly_version}/genome.fa"
    params.genome_sizes = "${_genome_base}/${_species}/${_assembly}/${_assembly_version}/genome.chrom.sizes"
    params.blacklist = "${_genome_base}/${_species}/${_assembly}/${_assembly_version}/blacklist.bed"
    params.atac_blacklist = "${_genome_base}/${_species}/${_assembly}/${_assembly_version}/atac.blacklist.bed"
    params.gtf          = "${_genome_base}/${_species}/${_assembly}/${_annotation}/${_annotation_version}/genes.gtf"
    params.bed          = "${_genome_base}/${_species}/${_assembly}/${_annotation}/${_annotation_version}/genes.bed"
    params.ensembl_genes          = "${_genome_base}/${_species}/${_assembly}/${_annotation}/gene_table.csv"
    params.ensembl_transcripts          = "${_genome_base}/${_species}/${_assembly}/${_annotation}/transcripts_table.csv"
    params.transcripts  = "${_genome_base}/${_species}/${_assembly}/${_annotation}/${_annotation_version}/transcripts.fa"
    params.salmon_index  = "${_genome_base}/${_species}/${_assembly}/${_annotation}/${_annotation_version}/SalmonIndex"
    params.star_index  = "${_genome_base}/${_species}/${_assembly}/${_annotation}/${_annotation_version}/STARIndex"

    params.bowtie2_index = "${_genome_base}/${_species}/${_assembly}/${_assembly_version}/bowtie2Index/genome"
    params.bwa_index = "${_genome_base}/${_species}/${_assembly}/${_assembly_version}/bwaIndex/genome.fa"
    
    params.commondb     = "${_share}/${_species}/${_assembly}/commondb/"
    params.bowtieInd_rRNA  = "${_share}/${_species}/${_assembly}/commondb/rRNA/rRNA"
    params.bowtieInd_ercc  = "${_share}/${_species}/${_assembly}/commondb/ercc/ercc"
    params.bowtieInd_miRNA = "${_share}/${_species}/${_assembly}/commondb/miRNA/miRNA"
    params.bowtieInd_tRNA  = "${_share}/${_species}/${_assembly}/commondb/tRNA/tRNA"
    params.bowtieInd_piRNA = "${_share}/${_species}/${_assembly}/commondb/piRNA/piRNA"
    params.bowtieInd_snRNA = "${_share}/${_species}/${_assembly}/commondb/snRNA/snRNA"
    params.bowtieInd_rmsk  = "${_share}/${_species}/${_assembly}/commondb/rmsk/rmsk"

    params.apa_utr = "${_genome_base}/apalyzer/${_assembly}.refUTRraw.csv"
    params.apa_intron = "${_genome_base}/apalyzer/${_assembly}.dfIPA.csv"
    params.apa_last_exon = "${_genome_base}/apalyzer/${_assembly}.dfLE.csv"

}

//* autofill