rnaseq-pipeline Requirements On Mac OS, these tools are best installed by conda. Probably same in Linux as well. fastqc fastp salmon Source URLs for bash command line argument parsing https://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash/14203146#14203146 https://dev.to/unfor19/parsing-command-line-arguments-in-bash-3b51