Run simple3 test (hv2s1) with 1k reads, and set simple1 test (h3s1) to auto chemistry

.gitlab-ci.yml

@@ -10,7 +10,7 @@ before_script:
   - mkdir test_data/mu.v3s2r10k
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s1r500/* test_data/hu.v3s1r500/
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v3s1r500/* test_data/mu.v3s1r500/
-  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r500/* test_data/hu.v2s1r500/
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r1k/* test_data/hu.v2s1r1k/
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v3s2r10k/* test_data/mu.v3s2r10k/
 
@@ -37,7 +37,7 @@ simple_1:
   except:
     - master
   script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
   - pytest -m count302
   artifacts:
     name: "$CI_JOB_NAME"
@@ -77,7 +77,7 @@ simple_3:
   except:
     - master
   script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r500/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
   - pytest -m count211
   artifacts:
     name: "$CI_JOB_NAME"