Try put ci pytest inline with inegrations

.gitlab-ci.yml

@@ -89,8 +89,7 @@ detailed_1:
     refs:
       - tags
   script:
-  - nextflow 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
+  - nextflow 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: "$CI_JOB_NAME"
     when: always
@@ -114,8 +113,7 @@ detailed_2:
     refs:
       - tags
   script:
-  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
-  - pytest -m count302
+  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2' && pytest -m count302
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -138,8 +136,7 @@ detailed_3:
     refs:
       - tags
   script:
-  - nextflow 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' -with-tower
-  - pytest -m count301
+  - nextflow 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: "$CI_JOB_NAME"
     when: always
@@ -162,8 +159,7 @@ detailed_4:
     refs:
       - tags
   script:
-  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1' -with-tower
-  - pytest -m count211
+  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1' && pytest -m count211
   artifacts:
     name: "$CI_JOB_NAME"
     when: always