nextflow.enable.dsl=2

process STAGE_DATA {
    container 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf'
    memory '2 GB'

    script:
    """
    BASE="/omic/eureka/digital-patients"
    
    echo "=== Cleaning up old _parts directories ==="
    find \$BASE -name "*_parts" -type d -exec rm -rf {} + 2>/dev/null || true
    echo "Cleanup done"
    
    echo "=== Current state of PVC ==="
    ls -la \$BASE/ 2>/dev/null || echo "Base dir missing"
    ls -la \$BASE/imputed/ 2>/dev/null || echo "imputed dir empty/missing"
    ls -la \$BASE/healthy/ 2>/dev/null || echo "healthy dir empty/missing"
    ls -la \$BASE/supporting-data/genome/ 2>/dev/null || echo "genome dir empty/missing"
    
    echo "=== Downloading files from alien server ==="
    apt-get update -qq && apt-get install -y -qq sshpass > /dev/null 2>&1 || true
    
    # Function to download via sshpass+scp
    download() {
        local remote="\$1"
        local local_path="\$2"
        mkdir -p \$(dirname "\$local_path")
        echo "Downloading: \$remote -> \$local_path"
        sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -P 9100 "omic@nucleus.omic.ai:\$remote" "\$local_path"
        ls -lh "\$local_path"
    }
    
    # Imputed files (schizophrenia)
    if [ ! -f "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz" ]; then
        download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz"
    else
        echo "SKIP: F5_SCHIZO both_sexes already present"
    fi
    
    if [ ! -f "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz" ]; then
        download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz"
    else
        echo "SKIP: F5_SCHIZO female already present"
    fi
    
    if [ ! -f "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz" ]; then
        download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz"
    else
        echo "SKIP: F5_SCHIZO male already present"
    fi
    
    # Gnomad files
    if [ ! -f "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt" ]; then
        download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.female.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt"
    else
        echo "SKIP: gnomad female already present"
    fi
    
    if [ ! -f "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt" ]; then
        download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.male.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt"
    else
        echo "SKIP: gnomad male already present"
    fi
    
    # hg38.fa (3.3GB)
    if [ ! -f "\$BASE/supporting-data/genome/hg38.fa" ]; then
        download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa" "\$BASE/supporting-data/genome/hg38.fa"
    else
        echo "SKIP: hg38.fa already present"
    fi
    
    echo "=== Final verification ==="
    echo "Imputed:"
    ls -lh \$BASE/imputed/*.bgz 2>/dev/null || echo "  NONE"
    echo "Healthy:"
    ls -lh \$BASE/healthy/*.txt 2>/dev/null || echo "  NONE"
    echo "Genome:"
    ls -lh \$BASE/supporting-data/genome/hg38.* 2>/dev/null || echo "  NONE"
    echo "Small files:"
    ls -lh \$BASE/MANE* \$BASE/regulon* \$BASE/LM22* \$BASE/ukbb* 2>/dev/null || echo "  NONE"
    
    echo "=== STAGING COMPLETE ==="
    """
}

workflow {
    STAGE_DATA()
}