Add arbitrary Dragen arguments

[adamrtalbot]

Description of feature

Currently we hard code the arguments supplied to Dragen for each process, however this runs the risk of becoming out of date or not supporting custom functions. In order to make the pipeline more flexible, we should include a method of users supplying custom arguments which are applied to the Dragen command line.

Note this can currently be achieved by setting the ext.args for each process, e.g. add this to a custom configuration file to remove optical duplicates:

process {
    withName: '.*:DRAGEN_DNA:DRAGEN' {
        ext.args = [
            '--enable-map-align true',
            '--enable-map-align-output true',
            '--enable-bam-indexing true',
            '--enable-sort=true',
            '--enable-duplicate-marking',    # Enable duplicate marking
            '--remove-duplicates',           # Remove duplicates
            '--enable-variant-caller true',
            '--enable-duplicate-marking true',
            '--output-format=BAM'
        ].join(" ")
}