install pip

.gitlab-ci.yml

 before_script:
   - module load astrocyte
   - module load python/3.6.1-2-anaconda
+  - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
   - module load nextflow/0.31.1_Ignite
   - mkdir -p test_data/simple1
   - mkdir -p test_data/simple2
@@ -28,7 +29,7 @@ simple_1FC:
     - tags
   script:
     - nextflow run workflow/main.nf --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv"
-#    - pytest -m design 
+    - pytest -m design
     - pytest -m untarBCL
     - pytest -m mkfastq
     - pytest -m fastqc
@@ -49,7 +50,7 @@ simple_2FC:
   stage: simple
   script:
     - nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
-#    - pytest -m design
+    - pytest -m design
     - pytest -m untarBCL
     - pytest -m mkfastq
     - pytest -m fastqc