I'm developing a pipeline with several nf-core modules feeding in to several local modules wrapping custom R scripts using nextflow.enable.moduleBinaries = true. It seems like whenever I add a module with a new script or change an existing script and run with resume, it doesn't pick up the cache and runs the whole pipeline. Is there a way to prevent this from happening by modifying something at either the pipeline or module level? Any suggestions are appreciated!

At least for the process where you changed the binary, this will alter the task hash and invalidate the cache. If this an early process, it will invalidate the cache for the downstream processes as well, if the receive an input that is an output of any of the affected processes.