Merge branch '14-ci' into 'develop'

Resolve "Develop CI"

See merge request !27

.gitlab-ci.yml

@@ -2,30 +2,38 @@ before_script:
   - module load astrocyte
   - module load python/3.6.1-2-anaconda
   - module load nextflow/0.31.1_Ignite
+  - mkdir test_data/hu.v2s1r500
   - mkdir test_data/mu.v2s2r10k
   - mkdir test_data/hu.v3s2r10k
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r500/* test_data/hu.v2s1r500/
   - 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
-  - run
+  - simple
+  - detailed
 
 astrocyte_check:
   stage: astrocyte
   script:
   - astrocyte_cli check ../cellranger_count
 
+run_hu.cr3v2ref3.0.0:
+  stage: simple
+  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 'GRCh38-3.0.0' --kitVersion 'two' --version '3.0.2'
+
 run_mu.cr2v2ref1.2.0:
-  stage: run
+  stage: detailed
   except:
     - tags
   script:
-  - 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 'mm10-1.2.0' --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 'mm10-1.2.0' --kitVersion 'auto' --version '2.1.1'
 
 run_hu.cr3v3ref3.0.0:
-  stage: run
+  stage: detailed
   except:
     - tags
   script:
-  - 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'
+  - 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 'auto' --version '3.0.2'