This capability was largely already in place, but this fixes a few minor issues and also expands this list of allowed flags. I've added some tests as well, however, I'm not systematically testing each option here (which would somewhat tedious). At least for now, it is up to the user to decide whether a particular option makes sense in the context of our pipeline.
This capability was largely already in place, but this fixes a few minor issues and also expands this list of allowed flags. I've added some tests as well, however, I'm not systematically testing each option here (which would somewhat tedious). At least for now, it is up to the user to decide whether a particular option makes sense in the context of our pipeline.
Closes #116