Enhancement: More control over output location

[schackartk]

It seems a bit restrictive to enforce that the output directory be structured as {workdir}/run{runnum}/. Most tools allow you to specify the output directory yourself.

This could be useful to the user (myself included) for organizing runs, and automating using a workflow manager. For instance, if I am running several combinations of aptamer, ligands, and modes, I may want my output directories to be {aptamer}/{ligand}/{mode}/. This structure is meaningful to me unlike the folder name "run1".

While this is not resolved in #8 , it would reduce the number of arguments. Instead of having both --workdir and --run_num, you could just have a single --outdir argument.

[taoliu032]

That's a good point! Here I think is where different users may have different preferences depending on their demands, etc.

A feature we currently have is that if the run_num is 0, the code will find out what the max run_num in the workdir made of "run*" folders, increment it by 1 and set the new run folder as run{max_num+1}, so that we don't need to explicitly set run_num every time. This is useful, for example, when quickly testing the pipeline multiple times and when it doesn't matter which molecules are being simulated. And these tests might all use the same combination of aptamer/ligand/mode.

On the other hand, the suggestion of {aptamer}/{ligand}/{mode}/ will be a lot favored when there are a bunch of different aptamers and/or ligands to test out. I think it'd be helpful to do this - perhaps {aptamer}/{ligand}/{mode}/{run} to distinguish different runs with different settings.

One concern is that aptamer (I suggest keeping --aptamer_seq to indicate it's DNA sequene as in my review comments) is the sequence which can go up to 40 or longer letters - maybe it's not an ideal name for a folder? To avoid this, there needs to be another CL argument like --aptamer_name to give it a shorter name.