83 lines
2.5 KiB
YAML
83 lines
2.5 KiB
YAML
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stages:
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- build_and_run
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- release
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image: ${IMAGE}
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variables:
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BASEIMAGE: ${CI_REGISTRY}/${CURRENT_TEMPLATE_IMAGE}
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.install-nextflow: &install-nextflow |
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wget -qO- https://get.nextflow.io | bash
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.install-conda: &install-conda |
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wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
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bash Miniconda3-latest-Linux-x86_64.sh -b -p ./miniconda
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source ./miniconda/bin/activate
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conda init
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conda-run:
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image: ubuntu:20.04
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stage: build_and_run
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before_script:
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- apt update && apt install -y wget default-jre
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- *install-nextflow
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- *install-conda
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script:
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- ./nextflow run workflow.nf
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-w ${OUTPUT}/workspace
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-profile conda
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--reads test_data/reads.fq.gz
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--out_dir ${OUTPUT}
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build-image:
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stage: build_and_run
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before_script:
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- apk add wget openjdk11 bash
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- *install-nextflow
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script:
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- echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
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- TAG="${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}"
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- docker build --no-cache -t "${TAG}" -f Dockerfile . --build-arg BASEIMAGE=${BASEIMAGE}
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# run letting nextflow orchestrate the containers
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- docker tag "${TAG}" "${CI_PROJECT_NAME}:latest"
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- OUTPUT="template-workflow"
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- ./nextflow run workflow.nf
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-w ${OUTPUT}/workspace
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-profile standard
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--reads test_data/reads.fq.gz
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--out_dir ${OUTPUT}
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# push
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- if [[ ${CI_COMMIT_BRANCH} == 'dev' ]]; then
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SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA};
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echo "Pushing ${SHATAG}";
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docker tag ${TAG} ${SHATAG};
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docker push ${SHATAG};
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fi;
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only:
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- branches
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artifacts:
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paths:
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# Add the output directory for the test
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- "template-workflow"
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expire_in: 1 day
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# Retag the image for git tags (releases)
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release:
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stage: release
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script:
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- echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
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- SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}
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- RELTAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_REF_NAME}
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- echo "Pulling ${SHATAG}"
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- docker pull ${SHATAG}
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- echo "Pushing ${TAG}"
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- docker tag ${SHATAG} ${RELTAG}
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- docker push ${RELTAG}
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only:
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- tags
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