Drop run ci to 2

.gitlab-ci.yml

@@ -4,34 +4,24 @@ before_script:
   - module load nextflow/0.31.1_Ignite
   - mkdir test_data/v2s2r100k
   - mkdir test_data/v3s2r100k
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v2s2r100k/* test_data/v2s2r100k/
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/* test_data/v3s2r100k/
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v2s2r10k/* test_data/mu.v2s2r10k/
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
 
 stages:
   - astrocyte
-  - integration
+  - run
 
 astrocyte_check:
   stage: astrocyte
   script:
   - astrocyte_cli check ../cellranger_count
 
-simple_cr2v2ref1.2.0:
-  stage: integration
+simple_mu.cr2v2ref1.2.0:
+  stage: run
   script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
 
-simple_cr2v2ref3.0.0:
-  stage: integration
+simple_hu.cr3v3ref3.0.0:
+  stage: run
   script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '2.1.1'
-
-simple_cr3v2ref3.0.0:
-  stage: integration
-  script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '3.0.2'
-
-simple_cr3v3ref3.0.0:
-  stage: integration
-  script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v3s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v3s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'