Develop

.gitlab-ci.yml

 before_script:
   - module load python/3.6.1-2-anaconda
-  - module load nextflow/0.27.6
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_count/*fastq.gz test_data/
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_count/design.csv test_data/
+  - 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/
 
 stages:
   - integration
 
-simple_test:
+simple_cr2v2ref1.2.0:
   stage: integration
   script:
-  - nextflow run workflow/main.nf
+  - 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'
+
+simple_cr2v2ref3.0.0:
+  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 = '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'