.gitlab-ci.yml

include:
    - project: "epi2melabs/ci-templates"
      file: "wf-containers.yaml"

variables:
    NF_WORKFLOW_OPTS: "--fastq test_data/fastq --samples test_data/sample_sheet.csv"
    NF_IGNORE_PROCESSES: "checkSampleSheet,combineGenotypeSummaries,genotypeSummary,report_no_data"
    CI_FLAVOUR: "new"
    # IMAGE_TAG: "NO_UPDATE"

# check-versions:
#   stage: pre-custom-builds
#   image: conda/miniconda3:latest
#   needs: []
#   script:
#     - apt-get update && apt-get -y install gcc
#     - pip install cachetools==4.1.0 docker==4.2.0 PyGithub==1.54 requests==2.20.0 semver==2.13.0 packaging
#     - python3 bin/check_aux_versions.py --docker_registry 'ontresearch/pangolin' --github_repository 'cov-lineages/pangolin' --token ${LABS_BOT_GH_TOKEN} --tool pangolin -p v > ./pangolin.txt
#     - python3 bin/check_aux_versions.py --docker_registry 'ontresearch/nextclade' --github_repository 'nextstrain/nextclade' --token ${LABS_BOT_GH_TOKEN} --tool nextclade > ./nextclade.txt
#   artifacts:
#     paths:
#       - pangolin.txt
#       - nextclade.txt
#     expire_in: 1 day
#   rules:
#       - if: '$CI_PIPELINE_SOURCE == "schedule"'
#
# .release:
#     stage: custom-builds
#     needs: ['check-versions']
#     before_script:
#         - export IMAGE_TAG=`cat ${FILE_NAME} | grep ACTION | cut -f2 -d":"`
#         - if [ "${IMAGE_TAG}" == "NO_UPDATE" ]; then echo "${IMAGE_NAME} already at latest version"; exit 0; fi;
#         - IMAGE_DOCKERFILE="${IMAGE_DOCKERFILE:-Dockerfile}"
#         - if [ -z "${IMAGE_NAME}" ]; then "IMAGE_NAME was not set"; exit 1; fi;
#         - if [ -z "${IMAGE_TAG}" ]; then "IMAGE_TAG was not set"; exit 1; fi;
#         - echo "Building auxiliary container with:"
#         - echo " - Dockerfile:'${IMAGE_DOCKERFILE}'"
#         - echo " - Image name:'${IMAGE_NAME}'"
#     script:
#         - !reference [.install, glibc-alpine]
#         - !reference [.install, awscli]
#         - echo ${DOCKERHUB_TOKEN} | docker login --username epi2melabs --password-stdin
#         - LATEST="${DOCKERHUB_NAMESPACE}/${IMAGE_NAME}:${IMAGE_TAG}"
#         - BUILD_CMD="docker build --no-cache -t ${LATEST} -f ${IMAGE_DOCKERFILE} . --build-arg IMAGE_TAG=${IMAGE_TAG}"
#         - echo "${BUILD_CMD}"
#         - ${BUILD_CMD}
#         - docker push ${LATEST}
#     rules:
#         - if: '$CI_PIPELINE_SOURCE == "schedule"'
#           when: on_success
#
# release-pangolin:
#   extends: .release
#   variables:
#     IMAGE_NAME: "pangolin"
#     FILE_NAME: "pangolin.txt"
#     IMAGE_DOCKERFILE: "Dockerfile_pangolin"
#
# release-nextclade:
#   extends: .release
#   variables:
#       IMAGE_NAME: "nextclade"
#       FILE_NAME: "nextclade.txt"
#       IMAGE_DOCKERFILE: "Dockerfile_nextclade"