Quality/coverage thresholds for gatk_find_covered_intervals in module-2

[allanbolipata]

From #273: Change thresholds for module-2.cwl. Also, ignore change variable naming in abra size calculation - it will be handled in #278

See 0018113

[allanbolipata]

These are actually already in! See https://github.com/mskcc/roslin-variant/blob/2.5.x/setup/cwl/modules/pair/realignment.cwl#L155-L158