A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I'm now training the qiime classifier with the input fasta and tax, but that takes ages (single threaded apparently)

In our original qiime2 bash script the qiime2 classifier is not used, but it uses the <https://docs.qiime2.org/2024.10/plugins/available/feature-classifier/classify-consensus-vsearch/|classify-consensus-vsearch> option
Would it be feasible/desirable to add that to the pipeline? I could see if I can get some time for it.
```qiime feature-classifier classify-consensus-vsearch \
  --i-query $output/$prefix.rep-seqs.ASV.qza \
  --i-reference-reads $SILVA_FASTA_LOCAL \
  --i-reference-taxonomy $SILVA_TAX_LOCAL \
  --p-threads $threads 
  --o-classification $output/$prefix.final-taxonomy_ASV.qza```
We would like to see if we can standardize more on ampliseq instead of our own local set of scripts for maintainability.

Make a GitHub issue (and assign yourself to it).