test singularity on CI

.gitlab-ci.yml

@@ -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

@@ -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
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