diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py
index 1342a125db90619ff19838d7cfb5c8c1be7b9d69..3df797b32c9d148a44f3b1e94fcdffd399cb63f8 100644
--- a/workflow/tests/test_annotate_peaks.py
+++ b/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
diff --git a/workflow/tests/test_generate_software_references.py b/workflow/tests/test_generate_software_references.py
index 3b6fe202b3361b4a2a71d79f0464f4e4c8962f7a..a627887eefe6359045abcefa54024f86e91d33d1 100644
--- a/workflow/tests/test_generate_software_references.py
+++ b/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/'
diff --git a/workflow/tests/test_generate_software_versions.py b/workflow/tests/test_generate_software_versions.py
index 77489a8c14ecf45c3ec90bd8b353b090ae7215fb..276fc9681a61999d71f246495691853b48c7efa4 100644
--- a/workflow/tests/test_generate_software_versions.py
+++ b/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/'
diff --git a/workflow/tests/test_overlap_peaks.py b/workflow/tests/test_overlap_peaks.py
index ff61c937f42af911bba8e8e21acde80bd41a592e..411bfd09ef3ebc437b7d90e75bcad3af2a8a7496 100644
--- a/workflow/tests/test_overlap_peaks.py
+++ b/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