Various renaming tasks

[dchiu911]

• Add zero-padding to repetition numbers so that scripts and logs are numerically sorted (e.g. "0001", "0002", ..., "1000")
• Load magrittr pipe once by storing in assets/utils.R and calling from parent scripts
• Rename directory R to pipeline since the pipeline contains more than just R scripts
• Rename workDir to scriptDir because working directory is really the scripts directory with R and bash scripts
• Use consistent successful/failure q() styles
• Pass whoami to path variables to improve more robust
• Use saveRDS and readRDS over the readr wrappers since we are not employing compression
• Use snake_case for all utility functions
• Pipeline specific utils.R should have all relevant functions and not nested in additional subdirectories

[dchiu911]

Unsupervised and Gene Selection outputs same as lock down master