Use contigs BED file for genomicsdb

[nvnieuwk]

Description of feature

Use contigs BED file for genomicsdb instead of the normal one. This way genomicsdb can be run more efficiently with --merge-contigs-into-num-partitions

[nvnieuwk]

Also update the arguments to improve the process for bigger and smaller batches (e.g =>)

    withName: "^.*JOINT_GENOTYPING:GENOMICSDBIMPORT\$" {
        time = "3d"
        memory = 200.GB
        cpus = 32
        ext.args = {
                    [
            "--batch-size 80",
                        "--overwrite-existing-genomicsdb-workspace true",
                        "--genomicsdb-shared-posixfs-optimizations true",
                        "--merge-input-intervals true",
                        "--bypass-feature-reader true",
            "--max-num-intervals-to-import-in-parallel 30",
            "--reader-threads 30",
            "--bypass-feature-reader",
            "--consolidate true"
                    ].join(" ")
                }
    }

[nvnieuwk]

Added in #144