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Klinische Genetica
capture-lumc
hutspot
Commits
e351fb2d
Commit
e351fb2d
authored
May 08, 2019
by
Sander Bollen
Browse files
test singularity on CI
parent
fef1b927
Pipeline
#2580
failed
Changes
2
Pipelines
1
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.gitlab-ci.yml
View file @
e351fb2d
...
...
@@ -30,6 +30,16 @@ test_dry_run:
-
docker
stage
:
dry-run
test_integration_singularity
:
<<
:
*docker_before_script_anchor
script
:
-
apt-get install singularity-container
-
py.test --tag singularity-integration
image
:
debian:buster
tags
:
-
docker
test_integration
:
before_script
:
-
export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)
...
...
tests/test_integration_run.yml
View file @
e351fb2d
...
...
@@ -18,3 +18,23 @@
-
"
rror"
tags
:
-
integration
-
name
:
test-singularity-integration-no-cluster
command
:
>-
bash -c '
snakemake --singularity --jobs 100 -w 120
-r -p -s Snakefile
--config REFERENCE=tests/data/ref.fa GATK=tests/data/ref.fa
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
:
-
singularity-integration
\ No newline at end of file
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