BioX::Workflow does the best it can to create an easy to parse directory structure.
Options are either files or directories, and for the most part can output looks like:
#Global indir - our raw data data/raw #Global outdir - our processed/analyzed data data/processed rule1 rule2 Or if by_sample_outdir data/processed Sample1/rule1 Sample1/rule2
Coerce relative path directories in variables: indir, outdir, and other variables ending in _dir to full path names
Print the workflow as 2 files.
#run-workflow.sh export SAMPLE=sampleN && ./run_things
Instead of each sample having its own command, have sample exported as an environmental variable.
This option is probably less ideal when working on an HPC cluster.
Make sure indir/outdirs are named appropriated for samples when using by