Hi,

This is the outline of your code

   # foreach (@Dirs)
   # foreach (@Dirs)
   # for ( 0 .. $#AbsDirs )
      # for ( 0 .. $#files )
   # for ( 0 .. $#AbsFiles )
      # if( $AbsFiles[$c] =~ /R2_001.fastq$/ )
         # while(<INPUT1>)
            # if( @readbuffer == 4 )
   # for ( 0 .. $#AbsFiles )
      # if( $AbsFiles[$d] =~ /R1_001.fastq$/ )
         # while(<INPUT2>)
            # if( @readbuffer == 4 )
               # if( exists( $input1{$key2} ) )
               # else
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This is how you should write code based on that outline

#!/usr/bin/perl --
use strict;
use warnings;
use File::Find::Rule qw/ find rule /;
use Path::Tiny qw/ path /;
my $root = path( grep defined, shift, '.' )->realpath;
for my $file ( find( name => qr/R2_001.fastq$/ , in => $root ) ){
    OneThing( $file );
}

for my $file ( find( name => qr/R1_001.fastq$/, in => $root ) ){
    TwoThing( $file );
}
exit 0;
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After looking closer at your while loops, this is how you should write that

for my $file ( find( name => qr/R2_001.fastq$/, in => $root ) ){
   SomeThing( $file );
}
exit 0;
sub SomeThing {
    my( $onein) = @_;
    my $twoin = $onein;
    $twoin =~ s/R2_001.fastq$/R1_001.fastq/;
    use Path::Tiny qw/ path /;
    my $out = path( $onein )->realpath( 'Output.fasta' );
    OneTwo( $onein, $twoin , $out );
}
sub OneTwo {
    my( $onein, $twoin, $out ) = @_;
    if( not path( $twoin )->exists ){
        warn qq{Skipping "$onein" because "$twoin" does not exist};
        return;
    }
    ...
}
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