wf-transcriptomes-v202/.gitlab-ci.yml

stages:
    - pretest
    - test
    - pre-release
    - release-checks 
    - 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    


# insist that the wfversion in nextflow.config matches the git tag
.check-versions: &check-versions |
    WFVER=$(grep "wfversion = " nextflow.config | awk '{gsub("\"","",$3); print $3}')
    TAGVER=${CI_COMMIT_TAG}
    if [[ "${TAGVER}" != "${WFVER}" ]]; then
        echo "Mismatching TAG and WORKFLOW versions:"
        echo " - TAG:$TAGVER"
        echo " -  WF:$WFVER"
        exit 1
    else
        echo "TAG and WORKFLOW versions agree: ${WFVER}"
    fi    

# Insist a CHANGELOG entry has been made for tags
.check-changelog: &check-changelog |
    TAGVER=${CI_COMMIT_TAG}
    MATCHES=$(grep -c "## \[${TAGVER}\]" CHANGELOG.md || exit 0)
    if [[ "${MATCHES}" != "1" ]]; then
        echo "Expected one match to '${CI_COMMIT_TAG}' in CHANGELOG, found ${MATCHES}"
        exit 1
    else
        echo "Found CHANGELOG.md entry for tag"
    fi    


# setup image for pushing to github
.setup-gh-push: &setup-gh-push |
    apt-get update -qq && apt-get install -y -qq git python3-all-dev git-lfs python3-venv
    mkdir ~/.ssh/
    cp $LABS_BOT_GH_KEY ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
    echo -e "Host github.com\n\tStrictHostKeyChecking no\n\tHostname ssh.github.com\n\tPort 443\n\n" > ~/.ssh/config
    git config --global user.email "epi2melabs@nanoporetech.com"
    git config --global user.name "epi2melabs-bot"    


conda-run:
    image: ubuntu:20.04
    stage: test
    before_script:
        - apt update && apt install -y wget default-jre
        - *install-nextflow
        - *install-conda
    script:
        - OUTPUT=${CI_PROJECT_NAME}
        - ./nextflow run main.nf
              -w ${OUTPUT}/workspace
              -profile conda
              --fastq test_data/reads.fq.gz 
              --out_dir ${OUTPUT}
    only:
        - branches


docker-run:
    stage: test
    before_script:
        - apk add wget openjdk11 bash
        - *install-nextflow
    script:
        # build image
        - TAG="${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:latest"
        - docker build --no-cache -t "${TAG}" -f Dockerfile . --build-arg BASEIMAGE=${BASEIMAGE}
        # run letting nextflow orchestrate the containers
        - OUTPUT=${CI_PROJECT_NAME}
        - ./nextflow run main.nf
              -w ${OUTPUT}/workspace
              -profile standard
              --wfversion latest
              --fastq test_data/reads.fq.gz 
              --out_dir ${OUTPUT}
        # push, to ont for later tagging, to dockerhub for release testing
        - if [[ ${CI_COMMIT_BRANCH} == 'dev' ]]; then
              echo "Pushing to ONT registry";
              echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY};
              SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA};
              echo " - tag is:${SHATAG}";
              docker tag ${TAG} ${SHATAG};
              docker push ${SHATAG};
              echo "Pushing to Dockerhub";
              echo ${DOCKERHUB_TOKEN} | docker login --username epi2melabs --password-stdin;
              HUBTAG="${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:${CI_COMMIT_SHORT_SHA}";
              echo " - tag is:${HUBTAG}";
              docker tag ${TAG} ${HUBTAG};
              docker push ${HUBTAG};
          fi;
    only:
        - branches
    artifacts:
        paths:
            # Add the output directory for the test
            - ${CI_PROJECT_NAME}
        expire_in: 1 day

###
# Push dev branch to github for release testers
release-dev:
    stage: pre-release
    image: $GH_PUSH_IMAGE
    before_script:
        - *setup-gh-push
    script:
        # Merge ont/dev into prerelease
        - git remote add ont ${CI_REPOSITORY_URL} || true
        - git remote add github git@github.com:epi2me-labs/${CI_PROJECT_NAME}.git || true
        - git fetch ont dev
        - git checkout ont/dev
        - git branch -D prerelease || echo "branch 'prerelease' not present"
        - git checkout -b prerelease
        # Edit nextflow config to set wfversion
        - grep 'wfversion = ".*"' nextflow.config || { echo "Failed to replace wfversion"; exit 1; }
        - sed -i 's/wfversion = ".*"/wfversion = "'${CI_COMMIT_SHORT_SHA}'"/' nextflow.config
        - git add nextflow.config
        - git commit -m "Setting wfversion to:${CI_COMMIT_SHORT_SHA}"
        - git push -f github prerelease
    only:
        - '/^dev$/'
    except:
        - tags

# Check things before release
release-checks:
    stage: release-checks
    script:
        - *check-versions
        - *check-changelog
    only:
        - tags


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

# Send all tags matching vX.Y.Z to github (code and release)
push-github:
    stage: release
    image: $GH_PUSH_IMAGE
    before_script:
        - *setup-gh-push
    script:
        # Push master and tag to github
        - git remote add ont ${CI_REPOSITORY_URL} || true
        - git remote add github git@github.com:epi2me-labs/${CI_PROJECT_NAME}.git || true
        - git fetch ont dev --tags
        - git fetch ont master
        - git fetch github master || echo "No 'master' branch present on github"
        - git checkout --track github/master || git checkout master
        - git merge ${CI_COMMIT_TAG}
        - git push github master
        - git push github ${CI_COMMIT_TAG}
        # Make a github release page
        - python3 -m venv release_env --prompt "(release) "
        - source release_env/bin/activate
        - pip install pip --upgrade
        - pip install git+https://github.com/epi2me-labs/github_release.git
        - github_release ${CI_PROJECT_NAME} ${CI_COMMIT_TAG} CHANGELOG.md ${LABS_BOT_GH_TOKEN}
    only:
        - /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/
    except:
        - branches