Added checking whether values of options are within range and removing some hardcoded paramters out of module files.
I checked whether -resume prevents nextflow from rerunning again if output files exist, but it still runs from the last process and overwrites files. I can't see any obvious alternatives within Nextflow. My feeling is that we leave this for now. As a user I would always assume the files would be overwritten, but would obviously have to think about this if for whatever reason it gets integrated in pathpipe.
Added checking whether values of options are within range and removing some hardcoded paramters out of module files.
I checked whether -resume prevents nextflow from rerunning again if output files exist, but it still runs from the last process and overwrites files. I can't see any obvious alternatives within Nextflow. My feeling is that we leave this for now. As a user I would always assume the files would be overwritten, but would obviously have to think about this if for whatever reason it gets integrated in pathpipe.