nf-core/tools API documentation
Automated documentation for nf-core/tools (1.13.2
)
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 bynxf_ver
in the test matrix:strategy: matrix: # Nextflow versions: check pipeline minimum and current latest nxf_ver: ['19.10.0', '']
NoteThese
matrix
variables run the test workflow twice, varying thenxf_ver
variable each time. This is used in thenextflow 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
- Development pipelines: