Skip any QC if reads are paired-end

At the moment the read-merge check performed at the beginning will run if `skip_merging_check` is set to false, even if the reads are paired-end. There should be a sanity check to catch this and either die at the beginning of the workflow, or warn and simply skip that step and any others requiring a merging check.

Since `skip_merging_check` defaults to true this isn't normally an issue.