Commit 96489f04 authored by Sander Bollen's avatar Sander Bollen
Browse files

functional test yml

parent 14eed9ee
Pipeline #2482 failed
......@@ -37,3 +37,16 @@ test_integration:
tags:
- slurm
stage: integration
test_functional:
before_script:
- export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)
script:
- source ${CONDA_SH}
- conda activate hutspot-pipeline
- py.test --tag functional --basetemp ${BASETEMP} --keep-workflow-wd
tags:
- slurm
stage: functional
only:
- schedules
\ No newline at end of file
- name: test-integration-run
command: >-
bash -c '
snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
--cluster 'sbatch' -r -p -s Snakefile -T
--config JAVA=$(which java)
REFERENCE=${FUNCTIONAL_REF} GATK=${GATK_JAR}
DBSNP=${FUNCTIONAL_DBSNP}
ONETHOUSAND=${FUNCTIONAL_ONETHOUSAND}
HAPMAP=${FUNCTIONAL_HAPMAP}
SAMPLE_CONFIG=${FUNCTIONAL_SAMPLE_CONFIG}'
exit_code: 0
stderr:
contains:
- "Job counts"
- "localrule all:"
- "(100%) done"
must_not_contain:
- "rror"
tags:
- functional
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