Workflow

Your workflow is a set of rules and conditions. Conditions come in two flavors, local and global. Local variables are local to a rule, and go away after that rule has been processed, while global live throughout each rule iteration.

Local and Global Variables

Global variables will always be available, but can be overwritten by local variables contained in your rules.

---
global:
    - indir: /home/user/example-workflow
    - outdir: /home/user/example-workflow/gemini-wrapper
    - file_rule: (.vcf)$|(.vcf.gz)$
    - some_variable: {$self->indir}/file_to_keep_handy
    - ext: txt
rules:
    - backup:
        local:
            - ext: "backup"
        process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.{$self->ext}.csv
    - rule2:
        process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.{$self->ext}.csv

Rules

Rules are processed in the order they appear.

Before any rules are processed, first the samples are found. These are grepped using File::Basename, the indir, and the file_rule variable. The default is to get rid of the everything after the final '.' .

Overriding Processes

By default your process is evaluated as

foreach my $sample (@{$self->samples}){
    #Get the value from the process key.
}

If instead you would like to use the infiles, or some other random process that has nothing to do with your samples, you can override the process template. Make sure to use the previously defined $OUT. For more information see the Text::Template man page.

rules:
    - backup:
        outdir: {$self->ROOT}/datafiles
        override_process: 1
        process: |
            $OUT .= wget {$self->some_globally_defined_parameter}
            {
            foreach my $infile (@{$self->infiles}){
                $OUT .= "dostuff $infile";
            }
            }