Export conda environment in Docker file

[drpatelh]

Would be nice to create a file with all of the packages used to create the Conda environment within the Docker container. This will be useful to recreate the same conda environment for downstream analysis in order to use the same tools (maybe add others), and hence adhere to reproducibility.

It should be as simple as translating and adding the command below into Docker language with the use of cookiecutter:
conda env export --name nf-core-atacseq-1.0.0 > nf-core-atacseq-1.0.0.yml

[ewels]

Docker language: Just add RUN before the bash statement. That's all :)

Would be nice to have it work for -profile conda as well though if possible...

[ewels]

@hpatel - going back over this, to clarify you mean because this pins all of the dependency package versions as well?

Should this file be saved to the pipeline results as well? Or is it sufficient to just have it inside the Docker container? Might be tricky to save it to results in such a way that still works if people are using homebrew software installations..

[drpatelh]

I think it's fine to have it inside the Docker container 👍 and then export the environment if required.

[drpatelh]

Itchy trigger finger 🔫 Still need to add the relevant RUN command to the Dockerfile in the pipeline template.

[ewels]

So... if the file is in the docker image, and you need to shell into the container to get to it. Then why don't you just shell into the container and export the environment yourself?

[drpatelh]

Because its easier to copy a file than to work out how to generate it 😅 Also, just so it can be said that all of the dependencies required to create the environment are in a file in the container. Not a biggie to be honest. Just thought it would help with transparency.