Young

Is there a fix for this coming? I also want to make a container, but I don't want to have to remove lines.

I have also encountered roary dropping samples. The first time that I noticed, I was only running roary with six samples. I reran my command. ``` roary \ -p 20...

Is it safe to assume that you are not currently working on a trycycler module? I'd like to get one going.

The typical commands for freyja are ``` # calls variants freyja variants \ !{bam} \ --variants freyja/!{sample}_variants.tsv \ --depths freyja/!{sample}_depths.tsv \ --ref !{reference_genome} # demix freyja demix \ freyja/!{sample}_variants.tsv \...

I'm converting this to draft until I get the test thing figured out.

I tried a few smaller genomes, but each option seemed like it would be too long. I've settled with using `test_toy.py` and I'm moving on with my life.

This is now ready for review

I'll push this to quay and dockerhub

I haven't answered, because I'm not sure what your question is. Generally, these can be used by any system that can use docker containers (or singularity). There are some systems...

This dockerfile looks very different from the prior version. This isn't a bad thing, it looks like augur has undergone a lot of changes, so it makes sense that the...