skip removing small fastq.gz files after the length filter with --list or --sample

[MarieLataretu]

Hi folks,

We have been using --fastq_pass --samples as input configuration, but we will switch to --fastq --list at some point. While testing, I noticed that the negative control didn't appear in the reports.

Now, I'm not sure if I understand the reasoning behind these lines completely: https://github.com/replikation/poreCov/blob/master/modules/filter_fastq_by_length.nf#L34-L36

However, we'd still like to have the negative control in the report, so with this PR, the removal of small fastq.gz files after the length filter is skipped with --list or --sample.

[replikation]

When using the e.g. 96 barcode kit you get tons of "false" barcodes. thats why we remove the small ones.

[hoelzer]

True, but I see that this is a problem when a negative control is included (which should have few reads, but people want to see it in the report)