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nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://nf-co.re/taxprofiler
MIT License
128 stars 36 forks source link

Update nonpareil to allow gzip input #502

Closed jfy133 closed 2 months ago

jfy133 commented 5 months ago

Description of feature

As this support has been added over the weekend

Thomieh73 commented 4 months ago

hey @jfy133 I was wondering, how can I use the nonpareil tool with taxprofiler? is that option available in the last public release, 1.1.8? I would very much like to use it in this workflow, when possible. Otherwise, I run it on the side.

jfy133 commented 4 months ago

Hi @Thomieh73

Nonpareil it is already is in our upcoming major release.

However note this version of nonpareil in that branch is the one without gzip support.

If you are happy to run with bleeding edge, you can try it by setting the pipeline version with -r bouncy-basenji.

Otherwise for now I recommend running it separately

Thomieh73 commented 4 months ago

Hi @jfy133 thanks for the quick response. Okay, I will try it out with using the version from bouncy-basenji, and see how that works. :-)

LilyAnderssonLee commented 2 months ago

Fixed in #515