BioX::Workflow::StructureOutput

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

Variables

coerce_paths

Coerce relative path directories in variables: indir, outdir, and other variables ending in _dir to full path names

min

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.

Subroutines

process_by_sample_outdir

Make sure indir/outdirs are named appropriated for samples when using by