integration tests in gitlab ci

.gitlab-ci.yml

-image: python:3.6-stretch
+.docker_before_script_anchor: &docker_before_script_anchor
+  before_script:
+    - pip install -r requirements.txt
+    - pip install -r requirements-dev.txt
 
-before_script:
-  - pip install -r requirements.txt
-  - pip install -r requirements-dev.txt
+stages:
+  - sanity
+  - dry-run
+  - integration
 
 test_sanities:
+  <<: *docker_before_script_anchor
   script:
     - py.test --tag sanity
+  image: python:3.6-stretch
   tags:
     - docker
+  stage: sanity
 
 test_dry_run:
+  <<: *docker_before_script_anchor
   script:
     - py.test --tag dry-run
+  image: python:3.6-stretch
   tags:
     - docker
+  stage: dry-run
+
+test_integration:
+  before_script:
+    - export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)
+  script:
+    - source ${CONDA_SH}
+    - conda activate hutspot-pipeline
+    - export PATH=${PATH}:${CONDA_EXTRA_PATH}
+    - py.test --tag integration --basetemp ${BASETEMP}
+  tags:
+    - slurm
+  stage: integration
\ No newline at end of file

tests/test_integration_run.yml

+- name: test-integration-run
+  command: >-
+    bash -c '
+    snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
+    --cluster 'sbatch' -r -p -s hutspot/Snakefile -T
+    --config JAVA=$(which java)
+    REFERENCE=tests/data/ref.fa GATK=${GATK_JAR}
+    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:
+    - integration