Change CI test to use new kitVersion

.gitlab-ci.yml

@@ -40,7 +40,7 @@ simple_1:
       - develop
       - master
   script:
-  - nextflow -bg 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 'three' --version '3.1.0' -with-tower
+  - nextflow -bg 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' -with-tower
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
@@ -65,7 +65,7 @@ simple_2:
       - master
       - tags
   script:
-  - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.1.0' -with-tower
+  - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
@@ -89,7 +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' -with-tower
+  - 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: "$CI_JOB_NAME"
@@ -114,7 +114,7 @@ detailed_2:
     refs:
       - tags
   script:
-  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2' -with-tower
+  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
   - pytest -m count302
   artifacts:
     name: "$CI_JOB_NAME"