Replace pytest

.gitlab-ci.yml

@@ -41,6 +41,7 @@ simple_1:
       - master
   script:
   - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+  - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -65,6 +66,7 @@ simple_2:
       - tags
   script:
   - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+  - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -88,6 +90,7 @@ detailed_1:
       - tags
   script:
   - nextflow -q run workflow/main.nf -profile biohpc,_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0'
+  - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -112,6 +115,7 @@ detailed_2:
       - tags
   script:
   - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+  - pytest -m count302
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -135,6 +139,7 @@ detailed_3:
       - tags
   script:
   - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
+  - pytest -m count301
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -158,6 +163,7 @@ detailed_4:
       - tags
   script:
   - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+  - pytest -m count211
   artifacts:
     name: "$CI_JOB_NAME"
     when: always