functional test yml

.gitlab-ci.yml

@@ -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

+- 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