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lib/BioX/Workflow/Example003.pod  view on Meta::CPAN

=encoding utf8


=head1 Example003

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.

In addition, it searches for samples by directory, and each outdir as
{$sample}/rule

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

 yaml
     ---
     global:
         - indir: /home/user/workflow/workflow/input
         - outdir: /home/user/workflow/workflow/output
         - file_rule: (.*)
         - find_by_dir: 1
         - by_sample_outdir: 1
     rules:
         - backup:
             process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
         - grep_VARA:
             process: |
                 echo "Working on {$self->{indir}}/{$sample.csv}"
                 grep -i "VARA" {$self->indir}/{$sample}.csv >> {$self->outdir}/{$sample}.grep_VARA.csv
         - grep_VARB:
             process: |
                 grep -i "VARB" {$self->indir}/{$sample}.grep_VARA.csv >> {$self->outdir}/{$sample}.grep_VARA.grep_VARB.csv


Make some test data

```yaml
    cd /home/user/workflow/input
    mkdir test1
    mkdir test2

    #Create test1.csv with some lines
    echo "This is VARA" >> test1/test1.csv
    echo "This is VARB" >> test1/test1.csv
    echo "This is VARC" >> test1/test1.csv
    
    #Create test2.csv with some lines
    echo "This is VARA" >> test2/test2.csv
    echo "This is VARB" >> test2/test2.csv
    echo "This is VARC" >> test2/test2.csv
    echo "This is some data I don't want" >> test2/test2.csv

```

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

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



=head2 Look at the directory structure

 bash
     /home/user/workflow/input
         test1/test1.csv
         test2/test2.csv
         /output
             /test1
                 /backup
                 /grep_vara
                 /grep_varb
             /test2
                 /backup
                 /grep_vara
                 /grep_varb



=head2 Run the workflow

Assuming you saved your output to workflow.sh if you run ./workflow.sh you will get the following.

 yaml
     /home/user/workflow/input
         test1/test1.csv
         test2/test2.csv
         /output
             /test1
                 /backup
                     test1.csv
                 /grep_vara
                     test1.grep_VARA.csv
                 /grep_varb
                     test1.grep_VARA.grep_VARB.csv
             /test2
                 /backup
                     test2.csv
                 /grep_vara
                     test2.grep_VARA.csv
                 /grep_varb
                     test2.grep_VARA.grep_VARB.csv