small fixes

.gitlab-ci.yml

@@ -34,6 +34,7 @@ test_dry_run:
 test_integration_singularity:
   before_script:
     - apt-get update && apt-get install -y python3-pip
+    - pip3 install pyfaidx
     - pip3 install -r requirements-dev.txt
   script:
     - py.test --tag singularity-integration

tests/test_integration_run.yml

@@ -21,7 +21,7 @@
 - name: test-singularity-integration-no-cluster
   command: >-
     bash -c '
-    snakemake --singularity --jobs 100 -w 120
+    snakemake --use-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