Incorporate delly filters as parameters

[YBerkovich]

In order to improve the call quality, implement some default parameters for SR and PE quality >= 5 leveraged in previous perl pipelines.

[timothyjsanders]

@tyamaguchi-ucla "Caden resolved this issue by allowing extra arguments. See https://github.com/uclahs-cds/pipeline-call-sSNV/blob/master/pipeline/modules/mutect2-processes.nf"