[workspace]
name = "bttoxin-pipeline"
channels = ["conda-forge", "bioconda", "bioconda/label/cf201901"]
platforms = ["linux-64"]
version = "0.1.0"
channel-priority = "disabled"

# =========================
# digger 环境：bioconda 依赖
# =========================
[feature.digger.dependencies]
bttoxin_digger = "==1.0.10"
perl = "==5.26.2"
perl-file-tee = "==0.07"
perl-list-util = "==1.38"
blast = "==2.16.0"

# =========================
# pipeline 环境：Python 分析依赖
# =========================
[feature.pipeline.dependencies]
python = ">=3.9"
pandas = ">=2.0.0"
matplotlib = ">=3.7.0"
seaborn = ">=0.12.2"

# =========================
# 环境定义
# =========================
[environments]
digger = ["digger"]
pipeline = ["pipeline"]

# =========================
# pixi tasks
# =========================
[feature.pipeline.tasks]
# 完整 pipeline（三阶段）
pipeline = "python scripts/run_single_fna_pipeline.py"
# 单独阶段
digger-only = "python scripts/run_digger_stage.py"
shotter = "python scripts/bttoxin_shoter.py"
plot = "python scripts/plot_shotter.py"