Sorry, me again. I just messed up a run because I had all my paths nested by 1 by accident, e.g. the parameter

alphafold2_small_bfd_path

was set to:

${params.alphafold2_db}/small_bfd/*

but was actually:

${params.alphafold2_db}/small_bfd/small_bfd/*

My fault, but it should error a bit earlier.