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Klinische Genetica
capture-lumc
hutspot
Commits
4aa40f5c
Commit
4aa40f5c
authored
Mar 26, 2019
by
Sander Bollen
Browse files
integration tests in gitlab ci
parent
06fe1fb7
Pipeline
#2477
failed with stages
in 1 minute and 47 seconds
Changes
2
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
.gitlab-ci.yml
View file @
4aa40f5c
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
tests/test_integration_run.yml
0 → 100644
View file @
4aa40f5c
-
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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