Our system is using HTCondor as a scheduler. It does not have a shared file system with the compute nodes. As a result, we must explicitly pass the input of each job through our submit command to the scheduler. Our scheduler transfer the input files manually to the compute node.

Is there a way we can pass through those file paths from NextDenovo? Is there a way, alternatively, to have the necessary files in each job copied to the /.work/<job_dir> (for example /01.raw_align/03.raw_align.sh.work/raw_align1? This way we would be able to move the entire directory during submission to the compute node.