#!/usr/bin/env nextflow
nextflow.enable.dsl=2

params.outdir = '/omic/eureka/digital-patients'

process DEBUG_PVC {
    container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'

    script:
    """
    echo "=== PVC mount check ==="
    echo "Current dir: \$(pwd)"
    echo ""
    echo "=== /omic/eureka contents ==="
    ls -la /omic/eureka/ 2>&1 | head -20
    echo ""
    echo "=== /omic/eureka/digital-patients/ ==="
    ls -la /omic/eureka/digital-patients/ 2>&1 | head -30
    echo ""
    echo "=== /omic/eureka/digital-patients/imputed/ ==="
    ls -la /omic/eureka/digital-patients/imputed/ 2>&1 | head -20
    echo ""
    echo "=== /omic/eureka/digital-patients/healthy/ ==="
    ls -la /omic/eureka/digital-patients/healthy/ 2>&1 | head -20
    echo ""
    echo "=== /omic/eureka/digital-patients/supporting-data/ ==="
    ls -laR /omic/eureka/digital-patients/supporting-data/ 2>&1 | head -30
    echo ""
    echo "=== Check for assembled files ==="
    ls -lh /omic/eureka/digital-patients/imputed/F5_SCHIZO* 2>&1
    ls -lh /omic/eureka/digital-patients/healthy/gnomad* 2>&1
    ls -lh /omic/eureka/digital-patients/supporting-data/genome/hg38* 2>&1
    echo ""
    echo "=== Small files check ==="
    ls -lh /omic/eureka/digital-patients/MANE* 2>&1
    ls -lh /omic/eureka/digital-patients/regulon* 2>&1
    ls -lh /omic/eureka/digital-patients/LM22* 2>&1
    ls -lh /omic/eureka/digital-patients/ukbb* 2>&1
    echo "=== DEBUG COMPLETE ==="
    """
}

workflow {
    DEBUG_PVC()
}