Refactor workflow inputs/output for consistency

[VJalili]

Workflows may have different input variable names for the same inputs, or the output variable name of one workflow may not match the input variable name of its downstream workflow where the output variable is piped to the input variable. For instance, both GatherSampleEvidence and EvidenceQC take a reference .fasta as input, but the variable names are different: GatherSampleEvidence.reference_fasta vs. EvidenceQC.genome_file.

While such inconsistencies do not have any functional impact, they can be confusing when preparing inputs to workflows (e.g., it is not clear from the variable name that reference_fasta and genome_file both expect the same input unless consulting with the configured Terra workspace or its corresponding templates), or setting up a new Terra workspace.

This PR makes the following refactoring:

• Remove EvidenceQC.genome_file as it is not used;
• EvidenceQC.counts, TrainGCNV.count_files, and MakeBincovMatrix.count_files to coverage_counts to match with GatherSampleEvidence;