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

// One-time script to reassemble chunked files on the PVC
// Run once, then delete. Not part of the main pipeline.

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

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

    script:
    """
    echo "=== Reassembling chunked files ==="

    # hg38.fa (35 parts)
    if [ -d "${params.base_dir}/supporting-data/genome/hg38.fa_parts" ]; then
        echo "Reassembling hg38.fa..."
        cat ${params.base_dir}/supporting-data/genome/hg38.fa_parts/part_* > ${params.base_dir}/supporting-data/genome/hg38.fa
        echo "  Done: \$(du -h ${params.base_dir}/supporting-data/genome/hg38.fa | cut -f1)"
    fi

    # gnomad male (12 parts)
    if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts" ]; then
        echo "Reassembling gnomad male..."
        cat ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts/part_* > ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt
        echo "  Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt | cut -f1)"
    fi

    # gnomad female (12 parts)
    if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts" ]; then
        echo "Reassembling gnomad female..."
        cat ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts/part_* > ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt
        echo "  Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt | cut -f1)"
    fi

    # F5_SCHIZO male (7 parts)
    if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts" ]; then
        echo "Reassembling F5_SCHIZO male..."
        cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz
        echo "  Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz | cut -f1)"
    fi

    # F5_SCHIZO female (7 parts)
    if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts" ]; then
        echo "Reassembling F5_SCHIZO female..."
        cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz
        echo "  Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz | cut -f1)"
    fi

    # F5_SCHIZO both_sexes (7 parts)
    if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz_parts" ]; then
        echo "Reassembling F5_SCHIZO both_sexes..."
        cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz
        echo "  Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz | cut -f1)"
    fi

    echo "=== All reassembly complete ==="
    """
}

workflow {
    REASSEMBLE()
}