Merge requests
Before making a pull request, make sure your module adheres to nf-core's new module guidelines which we follow too. For any questions, concerns or issues, please message either Matthieu (mm49) or Priyanka (ps22).
nf-core-modules directory
- Linting
nf-core modules lint <software/tool> --dir .
Repeat the above command till you have all errors resolved.
- Testing
TMPDIR=~ PROFILE=singularity pytest --tag <software/tool> --symlink --keep-workflow-wd --git-aware
- Staging
git add ./modules/<software_tool> ./tests/modules/<software_tool> ./tests/config/pytest_modules.yml
- Commit changes
git commit -m "Adding module for <software/tool>. Closes #<issue_number>."
- Push changes
git push -u origin <software_tool>
- Create a pull-request (PR)
- Go to https://github.com/sanger-tol/nf-core-modules/compare
- Set base branch to
sanger-tol/nf-core-modules:main - Set compare to
sanger-tol/nf-core-modules:<software_tool> - Click on "Create pull request"
- Fill out the template. Please check all boxes that apply, it helps with the review. Fill in
Closes #XXX, it helps with automation.
- Internal review
The review process is a back and forth collaborative exercise. Once complete, your PR is merged and the issue is closed.
Going through the PR review in nf-core is a personal choice. But creating the PR in nf-core/modules (1) ensures you get the credit if this module is further developed, and (2) helps ensuring that the module that ends up in nf-core is aligned to ours (e.g. input and output names).
It's also the way of contributing to a community that helps us out by providing tooling and modules.
- Create an issue for a new module
Go to nf-core/modules
- Create a new PR for
nf-core/modules
-
Click
compare across forks -
Set base branch to
nf-core/modules:master -
Set compare to
sanger-tol/nf-core-modules:<software_tool> -
Click on the arrow next to "Create pull request" and select "Create draft pull request"
-
Fill out the template. Please check all boxes that apply and fill in
Closes #XXX.
- Review