Added print help and ci/cd

[jadenseangmany]

• Prints help text from the readme when running snakemake test --cores x.
• Made small changes in the Snakefile to allow the fastq directory to not be parsed when we're running the test rule that prints the help commands.
• Some of the changes includes adding a new helper function that takes in already existing logic, and just putting it inside the helper which would allow the code to prevent the checks from running at the beginning when running test.