Commit e351fb2d authored by Sander Bollen's avatar Sander Bollen
Browse files

test singularity on CI

parent fef1b927
Pipeline #2580 failed
...@@ -30,6 +30,16 @@ test_dry_run: ...@@ -30,6 +30,16 @@ test_dry_run:
- docker - docker
stage: dry-run 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: test_integration:
before_script: before_script:
- export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d) - export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)
......
...@@ -18,3 +18,23 @@ ...@@ -18,3 +18,23 @@
- "rror" - "rror"
tags: tags:
- integration - 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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