misc_tasks.txt

# Generate balanced and unbalanced cooler files
#call cooler {input: set_id = set_id, all_valid_pairs = hicpro_merge.all_valid_pairs, genome_size = genome_size, bin_size=bin_size, monitoring_script = monitoring_script, disk_gb = 5000}


task cooler {
    String set_id
    File all_valid_pairs
    String genome_size
    String bin_size
    
    Int disk_gb  
    File monitoring_script

    command <<<

        chmod u+x ${monitoring_script}
        ${monitoring_script} > monitoring.log &
    
        echo`date`: Choosing smallest bin size of ${bin_size}
        RES=$(echo "${bin_size}" | tr " " "\n" | sort | head -n1)
    
        echo `date`: Starting makebins
        cooler makebins /annotation/${genome_size} $RES > bins.bed

        echo `date`: Starting cooler csort
        cooler csort --nproc 3 --chrom1 2 --pos1 3 --chrom2 5 --pos2 6 \
             -o allValidPairs.sorted  ${all_valid_pairs} /annotation/${genome_size}

        echo `date`: Starting cooler cload pairix
        cooler cload pairix bins.bed allValidPairs.sorted ${set_id}.cool

        echo "`date`: Starting cooler zoomify (unbalanced)"
        cooler zoomify --no-balance --out ${set_id}.mcool ${set_id}.cool

        echo "`date`: Starting cooler zoomify (balanced)"
        cooler zoomify --balance --out ${set_id}.balanced.mcool ${set_id}.cool

        echo `date`: Done
    >>>

    runtime {
        continueOnReturnCode: false    
        docker: "aryeelab/cooler:latest"
        memory: "32GB"
        disks: "local-disk " + disk_gb + " HDD"        

    }
    
    output {
        File mcool = "${set_id}.mcool"
        File monitoring_log = "monitoring.log"
    }
}