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

    ---
    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

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

The Structure

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