loving this pipeline :D revision 1.3.1, a set of 1500 seqs ended up with one group and one hmm profile.

NFCORE_PROTEINFAMILIES_PROTEINFAMILIES_REMOVE_REDUNDANCY_IDENTIFY_REDUNDANT_FAMS

emits an empty

redundant_fam_ids

and later

NFCORE_PROTEINFAMILIES:PROTEINFAMILIES:REMOVE_REDUNDANCY:FILTER_NON_REDUNDANT_FASTA

fails nagging

Missing output file(s)

. expected? issue?

Happy to hear that! A v2.0.0 of the pipeline with further updates such as extra QC/pre-processing and the possibility to merge similar families will be hopefully up by the end of this week!

fantastic, looking forward to try that out

first thing to check passes; redundant_fam_ids can be empty without problem. I will try to replicate a 1-family run, to see if that might be causing the error

Thanks, is v2 on dev branch? or you have a pre-release, I can check that out if it is almost baked

In the meantime you can skip the redundancy removal mechanism (since you dont have any) by setting the

--remove_family_redundancy

flag to

false

sure, thanks

ok, easy fix, will push and let you know when live