Currently if you have a single preprocessed input file that has paired reads in it (alternating forward and reverse reads), those reads are erroneously processed as single-end reads by some of the scripts. There is a step at the beginning of the workflow that scans through the input file(s) and tries to determine whether the reads are paired-end or single-end. That step correctly determines that the reads are paired-end, but we're not saving the config file after that step, so that information is lost.
Currently if you have a single preprocessed input file that has paired reads in it (alternating forward and reverse reads), those reads are erroneously processed as single-end reads by some of the scripts. There is a step at the beginning of the workflow that scans through the input file(s) and tries to determine whether the reads are paired-end or single-end. That step correctly determines that the reads are paired-end, but we're not saving the config file after that step, so that information is lost.