diff --git a/.gitignore b/.gitignore
index eb94944ee1efc2ed6d8571d51ad1bb7245c354ed..bf385c65b78082fb3581d2a2f613ae4da90d7d4b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -100,3 +100,13 @@ ENV/
 
 # Mac OS
 .DS_Store
+
+# nextflow analysis folders/files
+pipeline_trace*.txt*
+.nextflow*.log*
+report*.html*
+timeline*.html*
+/workflow/output/*
+/work/*
+/test_data/*
+/.nextflow/*
diff --git a/workflow/tests/test_generate_software_references.py b/workflow/tests/test_generate_software_references.py
index 916f891e71f0579c122ce5399981eb14b2309951..4d0025dfc3a925d2ec0d7bcd2bae86529d75e574 100644
--- a/workflow/tests/test_generate_software_references.py
+++ b/workflow/tests/test_generate_software_references.py
@@ -20,4 +20,4 @@ def test_software_references_output():
     with open(software_references, 'r') as stream:
         data_loaded = yaml.load(stream)
 
-    assert len(data_loaded['data'].split('<ul>')) == 18
+    assert len(data_loaded['data'].split('<ul>')) == 19