#11: Development environments & workflows

Phil Ewels /

Overview

• Image Not Showing Possible Reasons

  • The image file may be corrupted
  • The server hosting the image is unavailable
  • The image path is incorrect
  • The image format is not supported

  Learn More →
  Git + GitHub configuration
• 💻 VSCode configuration
• 💥 Pipeline testing

Git + GitHub configuration

• Image Not Showing Possible Reasons

  • The image file may be corrupted
  • The server hosting the image is unavailable
  • The image path is incorrect
  • The image format is not supported

  Learn More →
  Set up your fork on GitHub
• 💾 Configure your local clone
• ♻️ Pull in updates
• 🚀 Work on other people's code

Git + GitHub configuration

Local clone setup

git clone git@github.com:username/repo.git
cd repo
git remote add upstream git@github.com:nf-core/repo.git

Git + GitHub configuration

Pull updates

git status # check if we have any uncommitted changes
git pull   # implicitly pulls default remote - origin
git pull upstream dev
git push   # implicity pushes to default remote - origin

Git + GitHub configuration

Do work

git checkout -b my_feature
git commit -am "I did a thing"
git push -u origin my_feature

remote:
remote: Create a pull request for 'my_feature' on GitHub by visiting:
remote:      https://github.com/user/repo/pull/new/my_feature
remote:

Git + GitHub configuration

Shortcuts

• gupdate - https://github.com/ewels/dotfiles
• gh pr checkout 123 - https://cli.github.com

VSCode configuration

• 💪 Autoformat all the things
• 💥 Merge conflicts
• ⚒️ Useful plugins

VSCode configuration

Plugins

• VSCode plugins: "nf-core-extensionpack" 🚀
• Also: 🌈🦄✨ indent-rainbow
  

Pipeline testing

• 📃 Running tests locally / CI test logs
• 🙈 Ignoring nf-core lint tests
• 🐳 Building Docker locally
• 😣 Troubleshooting conda / inside containers

Ignoring nf-core lint tests

.nf-core-lint.yml

lint_test_name: False
other_test:
  - file_name.nf
  - for_example.txt

https://nf-co.re/tools-docs/lint_tests/

Building Docker locally

docker build . -t nfcore/mypipeline:dev
docker tag nfcore/mypipeline:dev nfcore/mypipeline:1.0.1

nfcore not nf-core! 😫

Troubleshooting conda

• 🐍 Just use mamba instead
• 💬 Ask for help on Bioconda Gitter

Troubleshooting inside containers

docker exec -it nfcore/mypipeline:dev sh