Add GitHub Actions to Template

[maxulysse]

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[maxulysse]

This PR is based on nf-core/sarek#27

[ewels]

SVG images are missing... But could probably just use shields.io anyway?

Travis stuff that I think we're still missing:

• Correct branch logic
  • If not from this repo, then must not be against master
  • If from repo and against master, then coming from dev
• That the changelog has been updated (maybe this is only the main tools repo, not pipelines?)

Would be good to have the branch stuff in it's own file / test I think? Would be super quick then and I like having the tests split up like that to make it super clear..

Great work!

[ewels]

From here:

You should put the following into your README which is supported directly by GitHub:

[![Actions Status](https://github.com/{owner}/{repo}/workflows/{workflow_name}/badge.svg)](https://github.com/{owner}/{repo}/actions)

[maxulysse]

Would be good to have the branch stuff in it's own file / test I think? Would be super quick then and I like having the tests split up like that to make it super clear..

Good point, I totally forgot about that one, I'll add that to the test on my sarek PR

From here:

That's exactly the link I used, I just figured one need to replace {owner}, {repo} and {workflow_name}, but I'm guessing it might have been working with the old Actions, and not this one, I'll keep looking

EDIT: Never mind, I found out how it works... It's pretty tricky in fact, for workflow_name you have to put indeed the workflow_name, wich is the name that you give the workflow in the yml file, and not the name of the yml file itself...

Here is how it works for Nextflow (the yml file being build.yml):
![Actions Status](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)

[maxulysse]

Nothing on shields.io yet, if I understood this issue: badges/shields#2574

[maxulysse]

I fixed the badges, and added a test to protect master: https://github.com/nf-core/tools/blob/2a959e24b530c551d52ce42c4c2b22a73e65a55e/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/.github/workflows/branch.yml

It's only triggered for master branch, and check that the GITHUB_AUTHOR is nf-core and that the head branch is dev, which should ensure the same test we were doing.

It should need further testing to verify that, so do not merge until we're sure with the Sarek PR.

[apeltzer]

Only question remaining for me: Are we dropping TravisCI in favor for this? Looks faster, more streamlined, better implemented and once you grasp the concept I don't see a reason to keep TravisCI tests in :D

[maxulysse]

I would say yes in the long term, but not now, it's still in beta :-D

[maxulysse]

Quick question about the branch protection.
So basically we allow PR to master only from dev, except if it's a patch/fix.
Should we have a specific name for such a branch?
Should have some docs about how to patch a pipeline?

[ewels]

Should we have a specific name for such a branch?

We do, it's patch right?

tools/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.travis.yml

Line 12 in 2d324b4

- '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))'

[ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]

[maxulysse]

Should we have a specific name for such a branch?

We do, it's patch right?

I know, the important part of the question was:

Should have some docs about how to patch a pipeline?

[apeltzer]

Yeah, having some docs on what / how we patch a pipeline would be good 👍

It shouldn't be used too often, though I hope 😆

[maxulysse]

I updated the CONTRIBUTING.md and related files.

[maxulysse]

Anyone has any idea why tests are failing on that one?

[ewels]

Couple of double cookiecutters are breaking the templating..

[maxulysse]

🤦‍♂️
Thanks a lot, I'm sure I was about to get there...

[maxulysse]

@ewels what do you think about the mergability of this one?

[ewels]

I'll review this if you guys review #467 and #465 😉

[ewels]

Looks great! I added a few minor suggested changes for docs and comment tweaks, but that's all.

Note that we'll need to update nf-core bump-version and nf-core lint, and also remove .travis.yml as part of that, but we can do that in a separate PR I guess.