Add argument to preventing halting when processing a batch

[liv-acollins]

When processing a set of files by specifying a directory to -s it would be helpful if the the process did not halt if a single raw file fails to run, e.g. due to the target or decoy file being empty. If this behaviour is preferred then an additional -skipOnFail argument could be added so that MSPathFinder continues to the next raw file.

[FarmGeek4Life]

Some changes to this effect will be implemented, however using a batch file of some sort will always be more robust.

[FarmGeek4Life]

What kind of errors are you currently seeing?

[liv-acollins]

Not an error as such. The halt occurs when no results have been found. Generally after a warning regards the target or decoy file is empty.

[FarmGeek4Life]

Hmm... Looking more at the code, it is supposed to continue processing spectrum files when one fails; if it isn't behaving that way, I will need more information (like a copy of the output, and maybe files and parameters).