So I think I found the issue, since im establishing a pipeline the -resume feature is often used. I decided to clean nextflow -f a couple of times. I reran the process and it worked. As I was looking at the cache system, Nextflow caches on name, size, last updated timestamp. Im sure since there was several resumes for this paricular step as i was editing my pipeline some piece of this information must have been broken so when umi_tools was looking for the index it was not able to find it.Clearing it to the last process that was successfully run helped. Looking at cache and its options could probably help as ‘leniant’ seems particularly useful for working on conflicting systems.