stages:
    - build_and_run
    - release

image: ${IMAGE}
variables:
    BASEIMAGE: ${CI_REGISTRY}/${CURRENT_TEMPLATE_IMAGE}

.install-nextflow: &install-nextflow |
    wget -qO- https://get.nextflow.io | bash

.install-conda: &install-conda |
    wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    bash Miniconda3-latest-Linux-x86_64.sh -b -p ./miniconda
    source ./miniconda/bin/activate
    conda init
    

conda-run:
    image: ubuntu:20.04
    stage: build_and_run
    before_script:
        - apt update && apt install -y wget default-jre
        - *install-nextflow
        - *install-conda
    script:
        - ./nextflow run workflow.nf
              -w ${OUTPUT}/workspace
              -profile conda
              --reads test_data/reads.fq.gz 
              --out_dir ${OUTPUT}


build-image:
    stage: build_and_run
    before_script:
        - apk add wget openjdk11 bash
        - *install-nextflow
    script:
        - echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
        - TAG="${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}"
        - docker build --no-cache -t "${TAG}" -f Dockerfile . --build-arg BASEIMAGE=${BASEIMAGE}
        # run letting nextflow orchestrate the containers
        - docker tag "${TAG}" "${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:latest"
        - OUTPUT="template-workflow"
        - ./nextflow run workflow.nf
              -w ${OUTPUT}/workspace
              -profile standard
              --reads test_data/reads.fq.gz 
              --out_dir ${OUTPUT}
        # push
        - if [[ ${CI_COMMIT_BRANCH} == 'dev' ]]; then
              SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA};
              echo "Pushing ${SHATAG}";
              docker tag ${TAG} ${SHATAG};
              docker push ${SHATAG};
          fi;
    only:
        - branches
    artifacts:
        paths:
            # Add the output directory for the test
            - "template-workflow"
        expire_in: 1 day


###
# Retag the image for git tags (releases)

.pull_tag: &pull_tag
    before_script:
        - echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
        - SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}
        - echo "Pulling ${SHATAG}"
        - docker pull ${SHATAG}
    only:
        - tags

# To ONT registry
release-int:
    stage: release
    <<: *pull_tag
    script:
        - echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
        - RELTAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_REF_NAME}
        - echo "Pushing ${TAG}"
        - docker tag ${SHATAG} ${RELTAG}
        - docker push ${RELTAG}

# To dockerhub
release-hub:
    stage: release
    <<: *pull_tag
    script:
        - echo ${DOCKERHUB_TOKEN} | docker login --username epi2melabs --password-stdin
        - RELTAG="${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:${CI_COMMIT_TAG}"
        - echo "Pushing ${RELTAG}"
        - docker tag ${SHATAG} ${RELTAG}
        - docker push ${RELTAG}