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Use smoke_de as default CI test

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Sam Nicholls 2026-06-09 12:04:53 +00:00
parent 1fa032ae0e
commit fbb1529816
1 changed files with 2 additions and 6 deletions
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8
.gitlab-ci.yml
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@ -4,12 +4,8 @@ include:
file: "wf-containers.yaml"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -nv -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -nv -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config"
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
--de_analysis --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
NF_BEFORE_SCRIPT: ":"
NF_WORKFLOW_OPTS: "--fastq test_data/smoke/de --sample_sheet test_data/smoke/sample_sheet_de.csv --ref_genome test_data/smoke/reference.fa --ref_annotation test_data/smoke/annotation.gtf --de_analysis --reference_level control --covariates batch"
CI_FLAVOUR: "new"
PYTEST_CONTAINER_NAME: "wf-common"
PYTEST_CONTAINER_CONFIG_KEY: "common_sha"