I used the LS on modules/nf-core/seqfu/check/main.nf Which changed this line:

def dirFlag = (reads instanceof List ? reads.every { read -> read.isDirectory() } : reads.isDirectory()) ? "--dir" : ""

to

def dirFlag = reads instanceof List ? reads.every { read -> read.isDirectory() } : reads.isDirectory() ? "--dir" : ""

Which led to this dirFlag being different in the execution when having a list. I did not want to spend more time on this, so I just reverted the changes for now. cf https://github.com/nf-core/modules/pull/10120/changes But if anyone wants to investigate this one, I have a feeling it's a fun one

That sounds like a bug to be honest

ok, I'll ping @Ben Sherman then