Michael Jahn

In your work directory for this module, rename `bacteria.name` to `bacteria.tax`. Then it will work. This is due to a change in the `kmerfinder` database structure. Strange enough, the `bacass`...

More specifically, this line in `modules/local/kmerfinder/main.nf` looks for both file endings: ``` def db_tax = file("${kmerfinderdb_path}/${tax_group}.name").exists() ? "${kmerfinderdb_path}/${tax_group}.name" : "${kmerfinderdb_path}/${tax_group}.tax" ``` I can not explain why it doesn't accept the...

I can confirm this; pipeline runs when using absolute instead of relative paths. I tried different relative paths but none seemed to work. I didn't exactly know which dir the...

I think if you want to run a single remote container with all conda envs installed in it, you need to use `container`. Add this line at the top of...

Hi! This is a known issue, your question is possibly a duplicate of #3490. The short answer is no, it is not possiby to use mamba without conda. You need...

thanks for doing this!

Hi @thomasmulvaney I had this idea/requirement too once in a while. But maybe this feature is too much out of the scope for the main snakemake code base. For me...

Hi, yes why not! I will test this as soon as I find time.

I just tested your repo, it's a good start! I installed it locally and tested it on different environment definition yaml files in `workflow/envs/.yml`. I had mixed results though. For...

Hi and thanks for your suggestion! However I don't fully understand the issue; can you give a reproducible example here, e.g. using the example data from the package? Is this...