Leandro Hermida

You can automate with workaround `yes y | kraken2-build`

For others coming here you don't need to specify double brackets in `expand` anymore for wildcards you want to keep in a partial expand, use single brackets and `allow_missing=True`

> @hermidalc do you have an example of this or a link to the docs? https://snakemake.readthedocs.io/en/stable/project_info/faq.html#i-don-t-want-expand-to-use-every-wildcard-what-can-i-do

This works with Kraken2 you just have to set it up yourself. You build two separate DBs from the same library types (e.g. bacteria, viral, etc), one for nucleotide and...

I'm having the same problem with 8.16.0. It's a documented feature but it doesn't work you can't actually specify e.g. `{params.wrapper}` or `{wildcards.wrapper}` in the wrapper directive!

> For `kraken2` I observed that performance is best at 1/2 to 3/4 of available cores. After that performance decreases. > > Not sure about if it is the same...

You are getting this error because your `Cluster9` input count matrix has samples with all zero counts. Remember samples are columns not rows in the count matrix, so you should...

Sorry, though why is there a warning? ```R library(clusterProfiler) library(enrichplot) library(msigdbr) data(geneList, package = "DOSE") m_t2g % dplyr::select(gs_name, entrez_gene) em

If you see in the Kraken2 FAQ https://github.com/DerrickWood/kraken2/wiki/FAQ#confidence-score > The authors of Kraken2 use the default confidence score of 0 for our own projects, preferring to use the minimizer score...

Issue still exists for me with kraken2 2.1.3 from conda. A workaround in cases where you aren't interactive do `yes y | kraken-build ...`