Many steps of the pipeline really include multiple steps, and it'd be nice to allow users to split these up. For example, smooth really has two parts:
Generate smoothed reads
Run LJA on these smoothed reads
I imagine that eventually someone's going to want to run step 2 without first running step 1 (e.g. LJA wasn't installed correctly, so step 2 failed, but there's no need to rerun step 1).
It's possible to set this up manually, but that might be a hassle. I think Click's group functionality should be able to handle this, but I am not very familiar with that so idk. Currently all of the commands are located in the strainflye "group", but presumably it's possible to put other groups within that (so the user could run a command like strainflye smooth to run both steps, or just strainflye smooth gen-reads or something).
Many steps of the pipeline really include multiple steps, and it'd be nice to allow users to split these up. For example,
smoothreally has two parts:I imagine that eventually someone's going to want to run step 2 without first running step 1 (e.g. LJA wasn't installed correctly, so step 2 failed, but there's no need to rerun step 1).
It's possible to set this up manually, but that might be a hassle. I think Click's group functionality should be able to handle this, but I am not very familiar with that so idk. Currently all of the commands are located in the strainflye "group", but presumably it's possible to put other groups within that (so the user could run a command like
strainflye smoothto run both steps, or juststrainflye smooth gen-readsor something).