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Klinische Genetica
capture-lumc
hutspot
Commits
96489f04
Commit
96489f04
authored
Mar 26, 2019
by
Sander Bollen
Browse files
functional test yml
parent
14eed9ee
Pipeline
#2482
failed
Changes
2
Pipelines
1
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.gitlab-ci.yml
View file @
96489f04
...
...
@@ -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
tests/test_functional_run.yml
0 → 100644
View file @
96489f04
-
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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