Merge branch '34-yaml_reader_fix' into 'master'

Update tests and import of yaml.

Closes #34

See merge request !24

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) == 152255
+    assert utils.count_lines(annotation_file) == 149284
 
 
 @pytest.mark.pairedend

workflow/tests/test_generate_software_references.py

@@ -3,6 +3,7 @@
 import pytest
 import os
 import utils
+import yaml
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/softwareReport/'

workflow/tests/test_generate_software_versions.py

@@ -3,6 +3,7 @@
 import pytest
 import os
 import utils
+import yaml
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/softwareReport/'

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) == 152262
+    assert utils.count_lines(peak_file) == 149291
 
 
 @pytest.mark.pairedend