jdidion
commented
6 years ago Thanks! Atropos actually does take a config file right now, it's just not documented yet. The format is pretty simple right now - just put one argument per line. The config file is loaded before parsing any command line arguments, so anything you specify on the command line overrides anything in the config file.
I like the idea of using a more structured config file. I might look at TOML or the tab-delimited format you suggest in a future release.
I like what you have done with this. I am also willing to help in anyway to keep this project moving forward. A suggestion I have is to use a tab delimited config file for inputting parameters something along the lines of the one I pasted below. The file can then be simply parsed into a named tuple and passed around easily. Even though the code is likely to break I would like some sort of API to allow simpler integration into my pipelines. I have started to play around with that but I am still very early into it. Again, let me know if there is something I might be able to help you with.
run_Mimir.txt