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.
At the moment the read-merge check performed at the beginning will run if
skip_merging_checkis 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_checkdefaults to true this isn't normally an issue.