SW-AmpIllumina-B optional visualizations updates

[torres-alexis]

• Moved the visualization script from workflow_code/scripts/ to new folder workflow_code/visualizations/
• Visualizations are now optional with the default being off.
• R-visualizations.log is now checked for and then copied to the outputs along with the other logs
• Visualizations can be enabled by either:
  • run_workflow.py launch: using the ‘--visualizations TRUE’ argument.
  • Direct snakemake launch: setting config[“enable_visualizations”] to “TRUE”
• Reformatted Snakefile rule all inputs (final outputs) to make addition of conditional outputs easier