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;
    }
    ...
}