Re: concatenate/stitch multiple GZip fastq files and output combined gzip file

[1nickt]

This:

    while (<IN>) {
        while ( my $line = IN ) {
          print $outputfile $line ;
        }
    }

should be this:

    while ( my $line = <IN> ) {
        print $outputfile $line ;
    }

But you should post the error you are getting here to give the Monks a chance to help without having to try to get your code to run.