37 lines
1.2 KiB
YAML
37 lines
1.2 KiB
YAML
# Include shared CI
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include:
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- project: "epi2melabs/ci-templates"
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file: "wf-containers.yaml"
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variables:
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# Workflow inputs given to nextflow.
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# The workflow should define `--out_dir`, the CI template sets this.
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# Only common file inputs and option values need to be given here
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# (not things such as -profile)
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NF_WORKFLOW_OPTS: "--fastq test_data"
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macos-run:
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stage: test
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script:
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- docker run hello-world
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- wget -qO- https://get.nextflow.io | bash
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# pull back the image
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- echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
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- docker pull ${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA}
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# run the workflow
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# custom scripting
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- echo "Running workflow specific script"
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- echo "Running:'${NF_BEFORE_SCRIPT}'"
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- eval ${NF_BEFORE_SCRIPT}
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# left for invididual project to control ${NF_WORKFLOW_OPTS}
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- CMD="./nextflow ${NF_RUN_OPTS_TAG_TEST} -profile standard ${NF_OUTPUT_OPTS} ${NF_WORKFLOW_OPTS}"
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- echo "Running:'${CMD}'"
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- ${CMD}
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needs:
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- ["docker-run"]
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only:
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- "/^dev$/"
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except:
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- tags
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