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.gitlab-ci.yml
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# Include shared CI
include:
- project: "epi2melabs/ci-templates"
file: "wf-containers.yaml"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq --references test_data/references --sample_sheet test_data/sample_sheet/sample_sheet.csv"
CI_FLAVOUR: "new"
PYTEST_CONTAINER_NAME: "wf-alignment"
docker-run:
tags: []
# Define a 1D job matrix to inject a variable named MATRIX_NAME into
# the CI environment, we can use the value of MATRIX_NAME to determine
# which options to apply as part of the rules block below
# NOTE There is a slightly cleaner way to define this matrix to include
# the variables, but it is broken when using long strings! See CW-756
parallel:
matrix:
- MATRIX_NAME: [
"fastq", "compress-one-ref"
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
# being incorrectly scheduled for "detached merge request pipelines" etc.
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
- if: $MATRIX_NAME == "fastq"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq --references test_data/references \
--sample_sheet test_data/sample_sheet/sample_sheet.csv -executor.\\$$local.memory 12GB"
# run on FASTQ again after compressing one / all references
- if: $MATRIX_NAME == "compress-one-ref"
variables:
NF_BEFORE_SCRIPT: "gzip test_data/references/lambda_757a991a.fasta"
NF_WORKFLOW_OPTS: "--fastq test_data/fastq --references test_data/references \
--sample_sheet test_data/sample_sheet/sample_sheet.csv -executor.\\$$local.memory 12GB"
aws-run:
parallel:
matrix:
- MATRIX_NAME: [ "fastq" ]
rules:
# NOTE As we're overriding the rules block for the included docker-run
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
# being incorrectly scheduled for "detached merge request pipelines" etc.
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
- if: $MATRIX_NAME == "fastq"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq --references test_data/references \
--sample_sheet test_data/sample_sheet/sample_sheet.csv -executor.\\$$local.memory 12GB"