# Organism to Genome Mapping for nf-core Pipelines
# Maps organism names (as they appear in GEO/SRA) to iGenomes keys

organisms:
  # Human
  "Homo sapiens":
    genome: "GRCh38"
    taxid: 9606
    aliases: ["human", "hg38", "GRCh38"]
    notes: "Primary human reference genome"

  "Homo sapiens (legacy)":
    genome: "GRCh37"
    taxid: 9606
    aliases: ["hg19", "GRCh37"]
    notes: "Legacy human reference, still used for some clinical data"

  # Mouse
  "Mus musculus":
    genome: "GRCm39"
    taxid: 10090
    aliases: ["mouse", "mm39", "GRCm39"]
    notes: "Current mouse reference genome"

  "Mus musculus (legacy)":
    genome: "GRCm38"
    taxid: 10090
    aliases: ["mm10", "GRCm38"]
    notes: "Legacy mouse reference"

  # Yeast
  "Saccharomyces cerevisiae":
    genome: "R64-1-1"
    taxid: 4932
    aliases: ["yeast", "sacCer3", "S288C", "budding yeast"]
    notes: "S288C reference strain"

  # Fruit fly
  "Drosophila melanogaster":
    genome: "BDGP6"
    taxid: 7227
    aliases: ["fly", "dm6", "fruit fly", "Dmel"]
    notes: "Berkeley Drosophila Genome Project release 6"

  # Worm
  "Caenorhabditis elegans":
    genome: "WBcel235"
    taxid: 6239
    aliases: ["worm", "ce11", "C. elegans", "Cele"]
    notes: "WormBase reference"

  # Zebrafish
  "Danio rerio":
    genome: "GRCz11"
    taxid: 7955
    aliases: ["zebrafish", "danRer11", "Drer"]
    notes: "Genome Reference Consortium Zebrafish Build 11"

  # Arabidopsis
  "Arabidopsis thaliana":
    genome: "TAIR10"
    taxid: 3702
    aliases: ["arabidopsis", "thale cress", "Atha"]
    notes: "The Arabidopsis Information Resource v10"

  # Rat
  "Rattus norvegicus":
    genome: "Rnor_6.0"
    taxid: 10116
    aliases: ["rat", "rn6", "Rnor"]
    notes: "Rnor 6.0 reference"

  # Chicken
  "Gallus gallus":
    genome: "GRCg6a"
    taxid: 9031
    aliases: ["chicken", "galGal6", "Ggal"]
    notes: "Genome Reference Consortium Chicken Build 6a"

  # Pig
  "Sus scrofa":
    genome: "Sscrofa11.1"
    taxid: 9823
    aliases: ["pig", "susScr11", "Sscr"]
    notes: "Swine genome assembly 11.1"

  # Cow
  "Bos taurus":
    genome: "ARS-UCD1.2"
    taxid: 9913
    aliases: ["cow", "bosTau9", "cattle", "Btau"]
    notes: "USDA ARS assembly"

  # Dog
  "Canis lupus familiaris":
    genome: "CanFam3.1"
    taxid: 9615
    aliases: ["dog", "canFam3", "Clup"]
    notes: "Broad Institute CanFam3.1"

  # Frog
  "Xenopus tropicalis":
    genome: "JGI_4.2"
    taxid: 8364
    aliases: ["frog", "xenTro9", "Xtro"]
    notes: "JGI assembly version 4.2"

  # Maize/Corn
  "Zea mays":
    genome: "Zm-B73-REFERENCE-NAM-5.0"
    taxid: 4577
    aliases: ["maize", "corn", "Zmay"]
    notes: "B73 reference genome v5"

  # Rice
  "Oryza sativa":
    genome: "IRGSP-1.0"
    taxid: 39947
    aliases: ["rice", "Osat"]
    notes: "International Rice Genome Sequencing Project"

  # E. coli (common bacterial model)
  "Escherichia coli":
    genome: null
    taxid: 562
    aliases: ["E. coli", "Ecol"]
    notes: "Use specific strain reference; K-12 MG1655 common"

  # Fission yeast
  "Schizosaccharomyces pombe":
    genome: "ASM294v2"
    taxid: 4896
    aliases: ["fission yeast", "S. pombe", "Spom"]
    notes: "PomBase reference"

# Pipeline mapping based on library strategy
pipeline_suggestions:
  "RNA-SEQ": "rnaseq"
  "ATAC-SEQ": "atacseq"
  "CHIP-SEQ": "chipseq"
  "WGS": "sarek"
  "WXS": "sarek"
  "EXOME": "sarek"
  "AMPLICON": "ampliseq"
  "BISULFITE-SEQ": "methylseq"
  "HI-C": "hic"
  "MIRNA-SEQ": "smrnaseq"
  "RRBS": "methylseq"