Migrate all modules to nf-test (batch 1)

[LouisLeNezet]

nf-test migration

(This is the first batch, batch 2 is here)

Some documentation available for this project:

• Slack channel
• Migration doc
• nf-test guidelines
• bytesize talk on nf-test
• bytesize talk on nf-test migration

Workflow

1. Create a conda environment.yml file with nf-core, nextflow, nf-test, prettier and pre-commit and activate it.
2. Run pre-commit install
3. Fork https://github.com/nf-core/modules
4. Clone the fork locally git clone [email protected]:githubusername/modules.git
5. Select the module you want to work on and assign yourself to the sub-issue below.
6. Update your local branch to match the nf-core repository git checkout main and git pull upstream main
7. Work on a branch git checkout -b <modules_name>_nftest
8. Run nf-core modules create <tool>/<subtool> --migrate-pytest
9. Check the migration and modify it accordingly
10. Run nf-core modules test <tool>/<subtool>
11. Lint the code nf-core modules lint <tool>/<subtool>
12. Commit the changes git add . and git commit -m "<commit_message>"
13. Push to your github repository git push origin <modules_name>_nftest
14. Open a Pull-Request and link it to the sub-issue
15. Check that github action run correctly
16. Fix if necessary
17. Ask for review and add the nf-test tag to the PR
18. Rinse and repeat 5 - 17