#!/usr/bin/env bash
set -e

# 1. Capture the target path from the first argument
TARGET_DIR=$1

if [ -z "$TARGET_DIR" ]; then
    echo "❌ Error: No path provided."
    echo "Usage: curl -s [URL] | bash -s -- path/to/my_project"
    exit 1
fi

echo "🚀 Initializing nf-core style project at: $TARGET_DIR"

# 2. Create the full directory structure
mkdir -p "$TARGET_DIR/workflows"
mkdir -p "$TARGET_DIR/modules"/{qc,alignment,sc,utils}
mkdir -p "$TARGET_DIR/conf/data_params"
mkdir -p "$TARGET_DIR/containers"/{docker,conda}
mkdir -p "$TARGET_DIR/envs/venvs"
mkdir -p "$TARGET_DIR/env_docs"
mkdir -p "$TARGET_DIR/data"/{raw,processed,reference}
mkdir -p "$TARGET_DIR/results/objects"/{anndata,seurat}
mkdir -p "$TARGET_DIR/results"/{tables,figures,logs}

# 3. Create placeholder files
touch "$TARGET_DIR/workflows/main.nf"
touch "$TARGET_DIR/conf/base.config"
touch "$TARGET_DIR/README.md"
touch "$TARGET_DIR/env_docs/README.md"

# 4. Create the YAML Template (The only file you edit per run)
cat <<EOF > "$TARGET_DIR/conf/data_params/dataset_v1.yaml"
# Single Cell Data Parameters
input_path: "data/raw/*.h5ad"
reference_path: "data/reference/genome.fa"
outdir: "results"
sample_id: "experiment_01"
EOF

# 5. Create .gitignore (To prevent uploading data/results to Git)
cat <<EOF > "$TARGET_DIR/.gitignore"
# Nextflow temporary files
.nextflow*
work/
.nextflow.log*

# Data and Results
data/raw/*
data/processed/*
results/*

# OS files
.DS_Store
EOF

# 6. Create .dockerignore
cat <<EOF > "$TARGET_DIR/.dockerignore"
.git
.nextflow
work/
data/
results/
EOF

# 7. Create basic nextflow.config
cat <<EOF > "$TARGET_DIR/nextflow.config"
params {
    input_path = "data/raw/*.h5ad"
    outdir     = "results"
}

profiles {
    docker { docker.enabled = true }
    conda  { conda.enabled  = true }
}

includeConfig 'conf/base.config'
EOF

echo "---"
echo "✅ Project successfully created at: $TARGET_DIR"
echo "📂 To start: cd $TARGET_DIR && code ."
echo "🧬 To run: nextflow run workflows/main.nf -params-file conf/data_params/dataset_v1.yaml"