Add stage_data.nf to download large files directly to PVC from alien server

stage_data.nf

@@ -0,0 +1,89 @@
+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()
+}