Variables that BioX::Workflow treats as special.
Directories - indir, outdir are looped. The indir of one rule is the outdir of the previous rule
Files - INPUT, OUTPUT are also looped. The INPUT of one rule is the OUTPUT of the previous.
INPUT and OUTPUT are used by the BioX::Workflow::Plugin::Drake and BioX::Workflow::Plugin::FileEixsts plugins.
Auto_name - Create outdirectory based on rulename
global: - outdir: /home/user/workflow/processed rule: normalize: process: dostuff {$self->indir}/{$sample}.in >> {$self->outdir}/$sample.out analyse: process: dostuff {$self->indir}/{$sample}.in >> {$self->outdir}/$sample.out
Would create your directory structure /home/user/workflow/processed/normalize (if it doesn't exist)
In addition each indir is the outdir of the previous rule
The indir of analyse (though not specified) is normalize.
This is similar to the auto_name function in the BioX::Workflow. Instead this says each INPUT should be the previous OUTPUT.
The initial indir is where samples are found
All output is written relative to the outdir
Special variables that can have input/output
These variables are also used in BioX::Workflow::Plugin::Drake
If we are using auto_input chain INPUT/OUTPUT
Set initial indir and outdir
For each sample the process is interpolated
{$sample}.csv -> Sample_A.csv
We need to set it back to the original for the following rule
To install BioX::Workflow, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioX::Workflow
CPAN shell
perl -MCPAN -e shell install BioX::Workflow
For more information on module installation, please visit the detailed CPAN module installation guide.