Add a single control end-end test.

.gitlab-ci.yml

@@ -8,6 +8,7 @@ stages:
   - unit
   - astrocyte
   - single
+  - control
   - multiple
   - skip
 
@@ -45,6 +46,15 @@ paired_end_human:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume
   - pytest -m pairedend
 
+single_end_single_control:
+  stage: single
+  only:
+    - branches
+  except:
+    - master
+  script:
+  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false -resume
+
 single_end_diff:
   stage: multiple
   only:

test_data/fetch_test_data.sh

@@ -25,3 +25,9 @@ wget https://www.encodeproject.org/files/ENCFF161HBP/@@download/ENCFF161HBP.fast
 wget https://www.encodeproject.org/files/ENCFF776KZU/@@download/ENCFF776KZU.fastq.gz
 wget https://www.encodeproject.org/files/ENCFF119KHM/@@download/ENCFF119KHM.fastq.gz
 echo "Done with Paired-end"
+
+echo "Downloading Single-end data set Human ENCSR000DXB and ENCSR000DXC"
+wget https://www.encodeproject.org/files/ENCFF001GBW/@@download/ENCFF001GBW.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF001GBV/@@download/ENCFF001GBV.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF001HWJ/@@download/ENCFF001HWJ.fastq.gz
+echo "Done with Single-end"

workflow/tests/test_pool_and_psuedoreplicate.py

@@ -72,6 +72,7 @@ def test_single_rep(design_experiment_2):
     single_rep = pool_and_psuedoreplicate.generate_design('false', 1.2, design_experiment_2, cwd, 1, 1)
     assert single_rep.shape[0] == 4
 
+
 @pytest.mark.singleend
 def test_pool_and_psuedoreplicate_singleend():
     design_file = os.path.join(test_output_path, 'ENCSR238SGC_ppr.tsv')