Merge branch '38-fix_bugs' into 'master'

Resolve "Missing modules"

Closes #38

See merge request !32

workflow/main.nf

@@ -326,6 +326,8 @@ process crossReads {
   }
   else {
     """
+    module load python/3.6.1-2-anaconda
+    module load phantompeakqualtools/1.2
     python3 $baseDir/scripts/xcor.py -t $seTagAlign
     """
   }

workflow/tests/test_annotate_peaks.py

@@ -24,7 +24,7 @@ def test_upsetplot_singleend():
 def test_annotation_singleend():
     annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 149284
+    assert utils.count_lines(annotation_file) == 152255
 
 
 @pytest.mark.pairedend

workflow/tests/test_generate_software_references.py

@@ -11,4 +11,13 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.singleend
 def test_software_references():
-    assert os.path.exists(os.path.join(test_output_path, 'software_references_mqc.txt'))
+    assert os.path.exists(os.path.join(test_output_path, 'software_references_mqc.yaml'))
+
+
+@pytest.mark.singleend
+def test_software_references_output():
+    software_references = os.path.join(test_output_path, 'software_references_mqc.yaml')
+    with open(software_references, 'r') as stream:
+        data_loaded = yaml.load(stream)
+
+    assert len(data_loaded['data'].split('<dt>')) == 17

workflow/tests/test_overlap_peaks.py

@@ -37,7 +37,7 @@ def test_check_update_design(design_diff):
 def test_overlap_peaks_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak'))
     peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak'
-    assert utils.count_lines(peak_file) == 149291
+    assert utils.count_lines(peak_file) == 152262
 
 
 @pytest.mark.pairedend