.gitlab-ci.yml

# 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)
    CI_FLAVOUR: "new"
    NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB --fastq test_data/fastq \
                        --reference_genome test_data/grch38/grch38_chr19_22.fa.gz \
                        --targets test_data/targets.bed --full_report --threads 4"


docker-run:
  tags: []

  # Define a 1D job matrix to inject a variable named MATRIX_NAME into
  #   the CI environment, we can use the value of MATRIX_NAME to determine
  #   which options to apply as part of the rules block below
  # NOTE There is a slightly cleaner way to define this matrix to include
  #   the variables, but it is broken when using long strings! See CW-756
  parallel:
    matrix:
      - MATRIX_NAME: ["multi-sample", "one-sample", "integration-test"]
  rules:
    # NOTE As we're overriding the rules block for the included docker-run
    #   we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
    #   being incorrectly scheduled for "detached merge request pipelines" etc.
    - if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
      when: never
    - if: $MATRIX_NAME == "multi-sample"
      variables:
        NF_WORKFLOW_OPTS:
          "-executor.\\$$local.memory 16GB --fastq test_data/fastq \
          --reference_genome test_data/grch38/grch38_chr19_22.fa.gz \
          --targets test_data/targets.bed --full_report --threads 4"
    - if: $MATRIX_NAME == "one-sample"
      variables:
        NF_WORKFLOW_OPTS:
          "-executor.\\$$local.memory 16GB --fastq 'test_data/fastq/sample_2/sample_2 ontarget.fastq.gz' \
          --reference_genome test_data/grch38/grch38_chr19_22.fa.gz \
          --targets test_data/targets.bed --full_report --threads 4"
    - if: $MATRIX_NAME == "integration-test"
      variables:
        NF_WORKFLOW_OPTS:
          "-executor.\\$$local.memory 16GB --fastq test/data/fastq/ \
          --reference_genome test/data/cas9_integration.fa \
          --targets test/data/cas9_integration.bed --full_report --threads 4"

integration_test:
  extends: .setup-alpine-nextflow
  dependencies: ["docker-run: [integration-test]"]
  stage: post-test
  script:
    - echo "ls" && ls
    - ls wf-cas9
    - SHA=$(./nextflow config -properties|grep ${PYTEST_CONTAINER_CONFIG_KEY}|awk -F= '{print $2}')
    - IMAGE="${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:${SHA}"
    - docker run -u $(id -u) -v ${PWD}:/host $IMAGE pytest /host/test/workflow_integration.py;