Update gitignore with nextflow and update software reference test

.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/*

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