testing using bats.

.gitlab-ci.yml

@@ -14,7 +14,8 @@ stages:
 user_configuration:
   stage: unit
   script:
-  - pytest -m unit
+  - module load singularity/3.0.2
+  - singularity run docker://bats/bats:v1.1.0 --tap workflow/tests/plot_profile.bats
   - pytest -m unit --cov=./workflow/scripts
 
 astrocyte:

workflow/tests/plot_profile.bats

 #!/opt/bats/libexec/bats-core/ bats
 
-profile_script="./worflow/scripts/plot_profile.sh"
+profile_script="./workflow/scripts/plot_profile.sh"
 
 setup() {
   module load deeptools/2.5.0.1
@@ -9,11 +9,4 @@ setup() {
 @test "Test deeptools present" {
   source ${profile_script}
   run check_tools
-  assert_success
-}
-
-@test "Test matrix generation" {
-  source ${profile_script}
-  run check_tools
-  assert_success
 }