Is there a way to pass parameters via command line?

[juancresc]

I would like to use the same script over and over but with different input variables, is there a way to pass arguments via command line?

[pcingola]

Yes, bds automatically parse command line for you on any global variable,
Here is the documentation and some examples: https://pcingola.github.io/BigDataScript/bigDataScript_manual.html#cmdLineParse