I was wondering if there is a way to force bacassto use a newer version of spades.py. When running unicycler separately, it show much better results when I used spades.py version 4.1 (or 4.2). But bacass always try v. 4.0. How or where can I force it to use a newer version? In my nextflow.config file I already use this to force a newer unicycler version, But I don't find any reference to spades.py in the whole repository/script.

withName:UNICYCLER {

container = '<https://depot.galaxyproject.org/singularity/unicycler:0.5.1--py312hdcc493e_4>'

//		container = '<https://depot.galaxyproject.org/singularity/spades:4.1.0--haf24da9_0>' # this throws an error

}

any help would be appreciated.

As far as I’m aware, bacass doesn’t have a standalone SPAdes module, so the only reliable way to run spades 4.1/4.2 is to find a version of Unicycler that already contains the newer spades version. 🤔

In the unicycler repository it mentions spades as a requirement. I don't think it comes with it.

Right. Because spades is a dependency, the image/environment bacass uses to run unicycler already includes it.

Ah, Isee, thanks. I'm using apptainer to run the pipeline. From what I can see, the latest unicycler version on the galaxy project singularity depot was done on Jan 25, while the spades version 4.1 was only published on Feb 2025. Is there a different way to get this container then the https://depot.galaxyproject.org/singularity/ site?

There is always the possibility to buildt your own container, or use conda and change the conda environment. But that seems a little excessive.

You could use this container for unicycler which has spades v4.1:

staphb/unicycler:0.5.1

from: https://hub.docker.com/r/staphb/unicycler/tags & dockerfile here: https://github.com/StaPH-B/docker-builds/tree/master/build-files/unicycler/0.5.1

Thanks @Curtis Kapsak, would it work by just changing the link in the config file?

So the docker image is pre-built and available on dockerhub. You can download it and convert it to apptainer format, then use that apptainer image in the nextflow workflow. Not sure exactly how to adjust the workflow config file, but it will essentially need to point at the apptainer image