BioX::Workflow uses a few conventions and special variables. As you probably noticed these are indir, outdir, infiles, and file_rule. In addition sample is the currently scoped sample. Infiles is not used by default, but is simply a store of all the original samples found when the script is first run, before any processes. In the above example the $self->infiles would evaluate as ['test1.csv', 'test2.csv'].
Variables are interpolated using Interpolation and Text::Template. All variables, unless explictly defined with "$my variable = "stuff"" in your process key, must be referenced with $self, and surrounded with brackets {}. Instead of $self->outdir, it should be {$self->outdir}. It is also possible to define variables with other variables in this way. Everything is referenced with $self in order to dynamically pass variables to Text::Template. The sample variable, $sample, is the exception because it is defined in the loop. In addition you can create INPUT/OUTPUT variables to clean up your process code. These are special variables that are also used in Drake. Please see BioX::Workflow::Plugin::Drake for more details.
---
global:
- ROOT: /home/user/workflow
- indir: {$self->ROOT}
- outdir: {$self->indir}/output
rules:
- backup:
local:
- INPUT: {$self->indir}/{$sample}.in
- OUTPUT: {$self->outdir}/{$sample}.out
Before version 0.03
This module was originally developed at and for Weill Cornell Medical College in Qatar within ITS Advanced Computing Team. With approval from WCMC-Q, this information was generalized and put on github, for which the authors would like to express their gratitude.
As of version 0.03:
This modules continuing development is supported by NYU Abu Dhabi in the Center for Genomics and Systems Biology. With approval from NYUAD, this information was generalized and put on bitbucket, for which the authors would like to express their gratitude.