Daniel Straub

Thats a nice suggestion I think. Optimally we would use an existing biocontainer of a dedicated tool. Do you know any such tool? I guess not, otherwise you wouldn't have...

Hi there, first thing that seems error prone is > Nextflow Version 21.08.0.edge Using an edge version can get quickly out of hand, those have often bugs and are intended...

Not solving you problem here, but I think we should change to https://github.com/oschwengers/bakta, because prokka seems to be not updated any more and bakta (at least from what I read)...

That's a little strange that the file contains no contigs at all. On the long run, it might be best to investigate how that happens and than correct that issue....

Revisiting this issue, the assembly was not good enough, no contig at all. Most likely the underlying data is insufficient. Nevertheless, it would be of advantage if the pipeline would...

I was not able to reproduce the error when using `NXF_VER=22.04.0 nextflow run nf-core/ampliseq -r 2.3.1 -profile test,cfc --outdir test` on our hpc where profile cfc can be found [here](https://github.com/nf-core/configs/blob/master/conf/cfc.config).

Problem: > [a5/e08cea] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE [100%] 1 of 1, failed: 1 I have used v2.3.1 now on multiple data sets and I havent had any trouble like this. As...

Since there is no other report of that problem, I have to assume its on your end. If anyone comes across that issue again, please report it.

So that could be either solved by QIIME2 with [`qiime feature-table group`](https://docs.qiime2.org/2021.8/plugins/available/feature-table/group/) or via phyloseq with [`merge_samples`](https://rdrr.io/bioc/phyloseq/man/merge_samples-methods.html).

That's in 2.4.0dev now.