Migrate all modules to nf-test (batch 2)

[LouisLeNezet]

Modules nf-test migration

(This is the second batch - batch 1 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
• pytest2nf-test automatic migration tool

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. Clone also locally pytest2nf-test git clone https://github.com/GallVp/pytest2nf-test
   • Install it cd pytest2nf-test + ./gradlew installDist
   • Add build to path or add alias alias pytest2nf-test=${PWD}/build/install/pytest2nf-test/bin/pytest2nf-test
6. Select the module you want to work on and assign yourself to the sub-issue below.
7. Update your local branch to match the nf-core repository git checkout main and git pull upstream main
8. Work on a branch git checkout -b <modules_name>_nftest
9. Run pytest2nf-test --nf-core-module <tool>/<subtool>
10. Check the migration and modify it accordingly
11. Run nf-core modules test <tool>/<subtool>
12. Lint the code nf-core modules lint <tool>/<subtool>
13. Commit the changes git add . and git commit -m "<commit_message>"
14. Push to your github repository git push origin <modules_name>_nftest
15. Open a Pull-Request and link it to the sub-issue by adding #75XX to the details
16. Check that github action run correctly
17. Fix if necessary
18. Ask for review and add the nf-test tag to the PR
19. Rinse and repeat 6 - 17