actions_ci

PipelineLint.actions_ci()

Checks that the GitHub Actions pipeline CI (Continuous Integration) workflow is valid.

The .github/workflows/ci.yml GitHub Actions workflow runs the pipeline on a minimal test dataset using -profile test to check that no breaking changes have been introduced. Final result files are not checked, just that the pipeline exists successfully.

This lint test checks this GitHub Actions workflow file for the following:

• Workflow must be triggered on the following events:

  on:
    push:
    branches:
      - dev
    pull_request:
    release:
    types: [published]

• The minimum Nextflow version specified in the pipeline’s nextflow.config matches that defined by nxf_ver in the test matrix:

  strategy:
    matrix:
      # Nextflow versions: check pipeline minimum and current latest
      nxf_ver: ['19.10.0', '']

  Note

  These matrix variables run the test workflow twice, varying the nxf_ver variable each time. This is used in the nextflow run commands to test the pipeline with both the latest available version of the pipeline ('') and the stated minimum required version.

• The Docker container for the pipeline must use the correct pipeline version number:

  • Development pipelines:

    docker tag nfcore/<pipeline_name>:dev nfcore/<pipeline_name>:dev

  • Released pipelines:

    docker tag nfcore/<pipeline_name>:dev nfcore/<pipeline_name>:<pipeline-version>

  • Complete example for a released pipeline called nf-core/example with version number 1.0.0:

    - name: Build new docker image
      if: env.GIT_DIFF
      run: docker build --no-cache . -t nfcore/example:1.0.0

  • name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/example
    docker tag nfcore/example
    nfcore/example:1.0.0