Example001

Here is a very simple example that searches a directory for *.csv files and creates an outdir /home/user/workflow/output if one doesn't exist.

Create the /home/user/workflow/workflow.yml

workflow.yml

 yaml
     ---
     global:
         - indir: /home/user/workflow
         - outdir: /home/user/workflow/output
         - file_rule: (.*).csv
     rules:
         - rule1:
             process: |
             Rule1
             INDIR: {$self->indir}
             OUTDIR: {$self->outdir}
         - rule2:
             process: |
             Rule2
             INDIR: {$self->indir}
             OUTDIR: {$self->outdir}
         - rule3:
             process: |
             Rule3
             INDIR: {$self->indir}
             OUTDIR: {$self->outdir}

Run the script to create out directory structure and workflow bash script

 bash
     biox-workflow.pl --workflow workflow.yml > workflow.sh

The Structure

    /home/user/workflow/
        test1.csv
        test2.csv
        /output
            /rule1
            /rule2
            /rule3