Commit 4aa40f5c authored by Sander Bollen's avatar Sander Bollen
Browse files

integration tests in gitlab ci

parent 06fe1fb7
Pipeline #2477 failed with stages
in 1 minute and 47 seconds
image: python:3.6-stretch
.docker_before_script_anchor: &docker_before_script_anchor
before_script:
- pip install -r requirements.txt
- pip install -r requirements-dev.txt
before_script:
- pip install -r requirements.txt
- pip install -r requirements-dev.txt
stages:
- sanity
- dry-run
- integration
test_sanities:
<<: *docker_before_script_anchor
script:
- py.test --tag sanity
image: python:3.6-stretch
tags:
- docker
stage: sanity
test_dry_run:
<<: *docker_before_script_anchor
script:
- py.test --tag dry-run
image: python:3.6-stretch
tags:
- docker
stage: dry-run
test_integration:
before_script:
- export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)
script:
- source ${CONDA_SH}
- conda activate hutspot-pipeline
- export PATH=${PATH}:${CONDA_EXTRA_PATH}
- py.test --tag integration --basetemp ${BASETEMP}
tags:
- slurm
stage: integration
\ No newline at end of file
- name: test-integration-run
command: >-
bash -c '
snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
--cluster 'sbatch' -r -p -s hutspot/Snakefile -T
--config JAVA=$(which java)
REFERENCE=tests/data/ref.fa GATK=${GATK_JAR}
DBSNP=tests/data/database.vcf.gz
ONETHOUSAND=tests/data/database.vcf.gz
HAPMAP=tests/data/database.vcf.gz
SAMPLE_CONFIG=tests/data/sample_config.json'
exit_code: 0
stderr:
contains:
- "Job counts"
- "localrule all:"
- "(100%) done"
must_not_contain:
- "rror"
tags:
- integration
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