learn make:

here are 3 examples I gave to my students (http://www.slideshare.net/lindenb/make-16134373 ). They all do the same job.

TRANSCRIPT=cat  # a tool that would convert a DNA to RNA stdin
TRANSLATE=cat # a tool that would translate a DNA from stdin
merged.protein: file1.pep file2.pep file3.pep
    cat file1.pep file2.pep \
        file3.pep > merged.protein

file1.pep: file1.rna
     ${TRANSLATE} file1.rna > file1.pep

file1.rna : file1.dna
    ${TRANSCRIPT} file1.dna > file1.rna

file1.dna:
    echo "ATGCTAGTAGATGC" > file1.dna

file2.pep: file2.rna
     ${TRANSLATE} file2.rna > file2.pep

file2.rna : file2.dna
    ${TRANSCRIPT} file2.dna > file2.rna

file2.dna:
    echo "ATGCTAGTAGATGC" > file2.dna


file3.pep: file3.rna
     ${TRANSLATE} file3.rna > file3.pep

file3.rna : file3.dna
    ${TRANSCRIPT} file3.dna > file3.rna

file3.dna:
    echo "ATGCTAGTAGATGC" > file3.dna

... a second example

TRANSCRIPT=cat
TRANSLATE=cat

%.pep:%.rna
    ${TRANSLATE} $< > $@
%.rna:%.dna
    ${TRANSCRIPT} $< > $@

merged.protein: file1.pep file2.pep file3.pep
    cat $^ > $@

file1.dna:
    echo "ATGCTAGTAGATGC" > $@
file2.dna:
    echo "ATGCTAGTAGATGC" > $@
file3.dna:
    echo "ATGCTAGTAGATGC" > $@

and a 3rd example:

TRANSCRIPT=cat
TRANSLATE=cat
INDEXES=1 2 3
%.pep:%.rna
    ${TRANSLATE} $< > $@
%.rna:%.dna
    ${TRANSCRIPT} $< > $@

merged.protein: $(foreach INDEX,${INDEXES},file${INDEX}.pep )
    cat $^ > $@

$(foreach INDEX,${INDEXES},$(eval \
file${INDEX}:\
    echo "ATGCTAGTAGATGC" > $$@ \
))

It is possible to write a shell script that runs your Perl scripts as a pipeline. For example, you have NGS data that needs to be trimmed, filtered, and mapped.

#BEGIN BASH SCRIPT
perl trimmer.pl data.fastq
perl filter.pl    data_trim.fastq
perl map.pl   data_trim_filt.fastq

And then to run it you type this in your terminal

bash perl_pipeline.sh

I started using a cluster to analyze my data and I find it useful to write shell scripts with dependencies in order to run hundreds of scripts in parallel. It's a powerful feeling.

Hope you liked this simple example!

Edit:

If you're really lazy like me, a good facet of a computational scientist, you'll write a Perl script to write the bash script. You can load the names of the files from their directory in the script and then write out commands in a loop like

foreach(@files){
    print OUT "perl perl_script.pl $_\n";
}

Have fun!

Have a look at Biopieces -> www.biopieces.org

This post may give you some idea about existing pipeline building framework:

C: Which bioinformatic friendly pipeline building framework?