nf-test migration

Edit

This project aims to finalise the transition of unit tests for all nf-core modules and sub-workflows to nf-test. It’s a good starting point for first timer to contribute and review Pull-Request.

Goal

1. Move all nf-core/modules to nf-test

• Batch 1
• Batch 2

2. Move all nf-core/subworkflows to nf-test

• Batch 1

More informations

• Pytest to nf-test migration documentation
• nf-test bitesize talk
• nf-test guidelines

How to proceed

As there are a lot of modules (i.e. 54) and subworkflows (i.e. 20) to migrate we need to stay organised to avoid duplicated work. To do so, we created three issues to track every contribution and a simple procedure as follows:

• Check if no one is already assigned to the modules/subworkflow you want to work on using one of the three main issues:
  • Modules Batch 1
  • Modules Batch 2
  • Subworkflows Batch 1
• Assign yourself to the sub-issue
• Perform the migration
  • Fork nf-core/modules repository to your Github account
  • Clone locally or use gitpod/codespaces
  • Clone pytest2nf-test git clone https://github.com/GallVp/pytest2nf-test
    • Install it ./gradlew installDist
    • Create alias or add to PATH: alias pytest2nf-test=${PWD}/build/install/pytest2nf-test/bin/pytest2nf-test
  • Go to modules repo and create a branch git checkout -b <tool_name>
  • Run pytest2nf-test --nfcore-modules <tool_name>
  • Run nf-core modules test <tool_name> -profile <singularity/docker/conda> and nf-core modules lint <tool_name>
  • Fix nf-test if necessary
  • Check if the module follows the guidelines
  • Commit changes and create Pull Request (PR) and link it to the sub-issue
• When your PR is ready, ask for a review and review someone else’s PR
• When merged update the Hackathon project
• Rinse and repeat!