Formatting improvements

[mwalker174]

To-be-addressed from https://github.com/talkowski-lab/gatk-sv-v1/pull/252:

• Some workflows currently require index files as inputs (e.g. module00c/CNMOPS). They should either be given default values or removed as inputs altogether.
• Some tasks require index files as inputs. This matters in some cases because tasks are called from other workflows, requiring passing the input files around (e.g. ClinicalFiltering.wdl::resetFilter line 392, called from GATKSVPipelineClinical).
• Because of the previous points, some workflows are still passing around index files. Note some index files have _idx in the file name, and some have _index
• Camel case convention: I think in most projects acronyms are treated as "words", hence CNMOPS -> Cnmops, GATKSVPipelinePhase1 -> GatkSvPipelinePhase1. We've just been treating them as a grey area. I don't think this is a big deal, but since you're going through and making a camel case fix, I wanted to take the time to get an explicit statement on how we treat acronyms.
• There are a few remaining references to "fam_file" instead of "ped_file" -- "runtime_override_merge_fam_file_list" in GATKSVPipelineClinical.wdl -- "cleaned_fam_file" in master_vcf_qc.wdl -- "fam_file" in several of the mosaic WDLs