From e829f60d95f91d66d7e577350e3d2c6aa4112a46 Mon Sep 17 00:00:00 2001
From: Chris Wright <chris.wright@nanoporetech.com>
Date: Tue, 16 Mar 2021 12:53:44 +0000
Subject: [PATCH] Switch to ci template

---
 .gitlab-ci.yml | 196 ++-----------------------------------------------
 1 file changed, 8 insertions(+), 188 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d5c54da..e54c2d4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,197 +1,17 @@
-stages:
-    - pretest
-    - test
-    - pre-release
-    - release-checks 
-    - release
+include:
+    - project: "epi2melabs/ci-templates"
+      file: "wf-containers.yaml"
 
-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"
-
+    RUN: "./nextflow run main.nf -w ${OUTPUT}/workspace --out_dir ${OUTPUT} --fastq test_data/reads.fq.gz"
 
 conda-run:
-    image: ubuntu:20.04
-    stage: test
-    before_script:
-        - apt update && apt install -y wget default-jre
-        - *install-nextflow
-        - *install-conda
+    extends: .conda-run
     script:
         - OUTPUT=${CI_PROJECT_NAME}
-        - ./nextflow run main.nf
-              -w ${OUTPUT}/workspace
-              -profile conda
-              --fastq test_data/reads.fq.gz 
-              --out_dir ${OUTPUT}
-    only:
-        - branches
-
+        - "${RUN} -profile conda"
 
 docker-run:
-    stage: test
-    before_script:
-        - apk add wget openjdk11 bash
-        - *install-nextflow
+    extends: .docker-run
     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
+        - "${RUN} -profile standard --wfversion latest"