# Include shared CI
include:
    - project: "epi2melabs/ci-templates"
      file: "wf-containers.yaml"

variables:
    # Workflow inputs given to nextflow.
    # The workflow should define `--out_dir`, the CI template sets this.
    # Only common file inputs and option values need to be given here
    # (not things such as -profile)
    NF_WORKFLOW_OPTS: "--fastq test_data"


macos-run:
    stage: test
    script:
        - docker run hello-world
        - wget -qO- https://get.nextflow.io | bash
        # pull back the image
        - echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
        - docker pull ${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}
        # run the workflow
        # custom scripting
        - echo "Running workflow specific script"
        - echo "Running:'${NF_BEFORE_SCRIPT}'"
        - eval ${NF_BEFORE_SCRIPT}
        # left for invididual project to control ${NF_WORKFLOW_OPTS}
        - CMD="./nextflow ${NF_RUN_OPTS_TAG_TEST} -profile standard ${NF_OUTPUT_OPTS} ${NF_WORKFLOW_OPTS}"
        - echo "Running:'${CMD}'"
        - ${CMD}
    needs:
        - ["docker-run"]
    only:
        - "/^dev$/"
    except:
        - tags