Gitlab ci

Add pytest-workflow tests and enable gitlab-ci integration, including the slurm runner.

.gitlab-ci.yml

@@ -5,6 +5,14 @@ variables:
   before_script:
     - pip3 install pytest-workflow
 
+.slurm_before_script_anchor: &slurm_before_script_anchor
+  before_script:
+    - export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID
+    - source ${CONDA_SH}
+    - conda activate vcf-to-varda
+    - export PATH=${PATH}:${SINGULARITY_PATH}
+    - echo $BASETEMP
+
 stages:
   - sanity
   - dry-run
@@ -19,9 +27,9 @@ test-sanity:
   stage: sanity
 
 test-dry-run:
-  <<: *before_script_anchor
+  <<: *slurm_before_script_anchor
   script:
-    - pytest --keep-workflow-wd-on-fail --tag dry-run
+    - pytest --keep-workflow-wd-on-fail --basetemp ${BASETEMP} --tag dry-run
   image: lumc/singularity-snakemake:3.5.2-5.15.0
   tags:
     - slurm