#!/usr/bin/env perl

use strict;
use warnings;

print '#!/bin/bash', "\n\n";

while (my $input = <>) { 
    chomp $input;
    if ( $input =~ / CS004_NoIndex_L002_R1_(\d+)\.fastq\.gz  /xms ) { 
        my $num = $1;
        print '    gunzip CS004_NoIndex_L002_R1_', $num, ".fastq.gz ;\n";
        print '    gunzip CS004_NoIndex_L002_R2_', $num, ".fastq.gz ;\n";
        print '    shuffleSequences_fastq.pl CS004_NoIndex_L002_R1_', 
              $num, 
              '.fastq CS004_NoIndex_L002_R2_', 
              $num, 
              '.fastq CS004_NoIndex_L002_R12_',
              $num, 
              ".fastq ;\n",
              ;
        print '    rm CS004_NoIndex_L002_R1_', $num, ".fastq.gz ;\n";
        print '    rm CS004_NoIndex_L002_R2_', $num, ".fastq.gz ;\n";
        print "\n";
    }
}