--aln-out unusable with deepclust

[vagkaratzas]

Hi!

I am converting diamond/deepclust to an nf-core module and I'm trying to capture possible optional outputs as well.

Regarding --aln-out, this is the command I tried:

diamond deepclust --memory-limit "4G" -p 2 --db UP000005640_9606.fasta --out human.tsv --aln-out human.aln

and got this error: Error: Alignment output to file is not supported without --parallel-tmpdir.

And then when adding that:

diamond deepclust --memory-limit "4G" -p 2 --db UP000005640_9606.fasta --out human.tsv --aln-out human.aln --parallel-tmpdir tmp

I get this error:

Error: Option is not permitted for this workflow: --parallel-tmpdir

Thanks!

[bbuchfink]

Should work if you use linclust instead of deepclust. --aln-out is more of an experimental option anyway and you may well skip it.