Get linting to pass

[vinisalazar]

Hi @nickp60,

Please excuse the massive PR. These are several small fixes to get the linting GitHub Actions to pass on the CI environment. I also updated the .devcontainer directory to the latest version used by nf-core/tools.

Could you check if GitHub Actions are enabled in this repo? This way we can make sure the linting action indeed passes.

Best,
Vini

[vinisalazar]

Still getting an error in tests (see vinisalazar#1), presumably due to the humann module downloading a container image during runtime.

[nickp60]

Hi @vinisalazar ! Thanks for putting all this together! I've now enabled the actions, hopefully those should kick in with your next commit. Overall it looks amazing, two minor requests:

• could you run a git rebase to clean up the history a bit since this has so many changes, some of which overlap with the current dev branch?
• In some places you've replaced branch names main with master -- could you revert those back to main?

I'll take a look at the container issue, but I think it might have to do with my module lacking -stub mode, which I can fix!

[vinisalazar]

Hey @nickp60, thanks for that

• Applied a git rebase using the dev branch from this fork. Let me know if you'd like to do anything else, eg. squash the commits further
• Pretty sure that change was due to a lint error. I will revert it and check the status, it might be the case of doing something to ignore that lint check. Edit: 623ed10

[vinisalazar]

@nickp60 I had a go with 235d870, but there's still container images being downloaded at runtime.

I'm presuming is the container mapping logic in the humann/base.nf module which is only evaluated at runtime

[nickp60]

Hi Vini, can you retry the rebase following the scheme laid out here? It looks like at some point the --force-with-lease arg needed to be used: I'm still seeing the PR's diff showing "changes" that already exist in dev.

Was the build_container directory added by the linter? I haven't see that in other nf-core pipelines, I'd assume that container would already be on some registry, rather than having to be built fresh each time.

Thanks again, sorry for the git spaghetti! And sorry for the delayed reply

[vinisalazar]

Hi Vini, can you retry the rebase following the scheme laid out here? It looks like at some point the --force-with-lease arg needed to be used: I'm still seeing the PR's diff showing "changes" that already exist in dev.

Hi Nick, just tried that, but not sure if it did any good. Could you be more specific as to what changes exactly already exist? I suspect there is some duplicated work on your fork, which I'm trying to sync by rebasing and it's causing conflicts.

Was the build_container directory added by the linter? I haven't see that in other nf-core pipelines, I'd assume that container would already be on some registry, rather than having to be built fresh each time.

Thanks, I think that came when updating .devcontainer setup, I removed it from the branch.

[nickp60]

Hi Vini, that appears to have fixed it, thanks! merging now so we can move on to other things, thanks again!