Move conda environment to yml

[edmundmiller]

Closes #4078

[edmundmiller]

Okay I have the changes for all of the modules locally. I'm not pushing it up yet because I don't want another PR with 100 reviewers 😬 https://github.com/Emiller88/modules/commit/5ca19f5ccb93da671323a9864f1aca30a5af231b

[edmundmiller]

Merging sorry for all the requests 😬

[ajtock]

Hi @emiller88

Would it be valid to make the conda directive path absolute rather than relative by adding "${projectDir}/" (e.g., conda "${projectDir}/modules/nf-core/trimgalore/environment.yml")? I encountered a potential issue when running a pipeline locally, where the relative path can be resolved only if the launch directory is the project directory containing modules/. I'm not too familiar with nf-test yet, but is it possible that adding "${projectDir}/" to the path might also fix Process relative paths aren't resolved correctly askimed/nf-test#146?

Thanks!
Andy

[nvnieuwk]

I think this is a better solution for the whole pipeline runs, but it doesn't fix nf-test since it creates a small pseudo workflow to test the process. That pipeline is located in the .nf-test folder so the $projectDir is there instead of the top folder. this will need a change in nf-test to work

[grst]

what about "${moduleDir}/environment.yaml"?

[nvnieuwk]

Wow this works! Thanks for the suggestion @grst !!

[nvnieuwk]

Fix PR: #4252