# Functional Annotation Skill Configuration
# 功能注释技能 - 使用 eggNOG-mapper 进行蛋白功能注释

skill:
  name: annotation
  version: "1.0.0"
  description: "功能注释分析 - eggNOG-mapper"
  author: "bbav20311-team"

input:
  protein_fasta: null  # 必需: 蛋白序列FASTA文件

parameters:
  emapper:
    # eggNOG-mapper 主要参数
    mode: "diamond"           # 搜索模式: diamond/mmseqs/hmmer
    evalue: 0.001             # E-value阈值
    score: 60                 # 最小bit score
    query_cover: 20           # 最小query覆盖度(%)
    subject_cover: 20         # 最小subject覆盖度(%)
    tax_scope: "auto"         # 分类范围: auto/bact/arch/euk/viruses
    go_evidence: "non-electronic"  # GO证据: all/non-electronic/experimental
    target_orthologs: "all"   # 目标直系同源: all/one2one/one2many
    # 数据库路径 (可选，默认使用 ~/.eggnog-mapper/)
    data_dir: null            # eggNOG 数据库目录，如 /path/to/eggnog_db
    # 性能参数
    cpu: 8
    block_size: 5             # Diamond block size (内存控制)
  
output:
  format: ["annotations", "seed_orthologs", "pfam", "cog", "kegg"]
  report_template: "templates/report.md.j2"
  include_reproducibility: true

dependencies:
  conda:
    channels:
      - bioconda
      - conda-forge
    packages:
      - eggnog-mapper=2.1.12
      - diamond=2.1.8
      - biopython=1.81
      - pandas=2.0.0