add spaceranger to CI and add to testdata location on shared folder

.gitlab-ci.yml

@@ -6,8 +6,10 @@ before_script:
   - module load singularity/3.5.3
   - mkdir -p test_data/simple1
   - mkdir -p test_data/simple2
+  - mkdir -p test_data/simple3
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/* test_data/simple1/
   - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple2/* test_data/simple2/
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple3/* test_data/simple3/
 
 stages:
   - astrocyte
@@ -27,7 +29,7 @@ astrocyte_check:
 simple_1FC:
   stage: simple
   script:
-    - nextflow run workflow/main.nf -profile biohpc,cluster --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
+    - nextflow run workflow/main.nf -profile biohpc,cluster --ranger "cellranger" --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
     ##- pytest -m simple1
   artifacts:
     name: "$CI_JOB_NAME"
@@ -44,7 +46,7 @@ simple_1FC:
 simple_2FC:
   stage: simple
   script:
-    - nextflow run workflow/main.nf -profile biohpc,cluster --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
+    - nextflow run workflow/main.nf -profile biohpc,cluster --ranger "cellranger" --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
     ##- pytest -m simple2
   artifacts:
     name: "$CI_JOB_NAME"
@@ -57,3 +59,20 @@ simple_2FC:
     max: 0
     when:
       - always
+
+simple_3FC:
+  stage: simple
+  script:
+    - nextflow run workflow/main.nf -profile biohpc,cluster --ranger "spaceranger" --bcl "test_data/simple3/*.tar.gz" --designFile "test_data/simple3/spaceranger-tiny-bcl-simple-1.0.0.csv" --ci true
+    ##- pytest -m simple3
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - .nextflow.log
+      - workflow/output/multiqc/run/multiqc_report.html
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always

workflow/tests/test_mkfastq.py

@@ -12,13 +12,17 @@ from io import StringIO
 import os
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-		'/../output/mkfastq/'
+		'/../output/'
 
 @pytest.mark.simple1
 def test_simple1_mkfastq():
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0', 'outs'))
+    assert os.path.exists(os.path.join(test_output_path, 'mkfastq', 'cellranger-tiny-bcl-1_2_0', 'outs'))
 
 @pytest.mark.simple2
 def test_simple2_mkfastq():
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-1', 'outs'))
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2', 'outs'))
\ No newline at end of file
+    assert os.path.exists(os.path.join(test_output_path, 'mkfastq', 'cellranger-tiny-bcl-1_2_0-1', 'outs'))
+    assert os.path.exists(os.path.join(test_output_path, 'mkfastq', 'cellranger-tiny-bcl-1_2_0-2', 'outs'))
+
+@pytest.mark.simple3
+def test_simple3_mkfastq():
+    assert os.path.exists(os.path.join(test_output_path, 'spaceranger_mkfastq', 'mkfastq_spaceranger-tiny-bcl-1', 'outs'))

workflow/tests/test_multiqc.py

@@ -20,4 +20,8 @@ def test_simple1_multiqc():
 
 @pytest.mark.simple2
 def test_simple2_multiqc():
-    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
\ No newline at end of file
+    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
+
+@pytest.mark.simple3
+def test_simple3_multiqc():
+    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))