diff --git a/histoqc/tests/coverage.xml b/histoqc/tests/coverage.xml
index 99bdf26..beb3109 100644
--- a/histoqc/tests/coverage.xml
+++ b/histoqc/tests/coverage.xml
@@ -1,12 +1,12 @@
 <?xml version="1.0" ?>
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 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
-		<source>/Users/nanli/Documents/github/HistoQC/histoqc</source>
+		<source>/home/nli31/github/nanli-emory/HistoQC/histoqc</source>
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 					<methods/>
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 					</lines>
 				</class>
-				<class name="_worker.py" filename="_worker.py" complexity="0" line-rate="0.6327" branch-rate="0">
+				<class name="_worker.py" filename="_worker.py" complexity="0" line-rate="0.6154" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="2" hits="1"/>
 						<line number="3" hits="1"/>
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 						<line number="5" hits="1"/>
 						<line number="6" hits="1"/>
 						<line number="7" hits="1"/>
 						<line number="12" hits="1"/>
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 						<line number="37" hits="1"/>
 						<line number="39" hits="1"/>
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 						<line number="46" hits="1"/>
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 				</class>
 			</classes>
@@ -2106,9 +2225,9 @@
 				</class>
 			</classes>
 		</package>
-		<package name="config" line-rate="0.9565" branch-rate="0" complexity="0">
+		<package name="config" line-rate="0.1304" branch-rate="0" complexity="0">
 			<classes>
-				<class name="__init__.py" filename="config/__init__.py" complexity="0" line-rate="1" branch-rate="0">
+				<class name="__init__.py" filename="config/__init__.py" complexity="0" line-rate="0.375" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="6" hits="1"/>
@@ -2116,59 +2235,59 @@
 						<line number="8" hits="1"/>
 						<line number="17" hits="1"/>
 						<line number="20" hits="1"/>
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-						<line number="29" hits="1"/>
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+						<line number="36" hits="0"/>
+						<line number="37" hits="0"/>
+						<line number="38" hits="0"/>
 					</lines>
 				</class>
-				<class name="__main__.py" filename="config/__main__.py" complexity="0" line-rate="0.9333" branch-rate="0">
+				<class name="__main__.py" filename="config/__main__.py" complexity="0" line-rate="0" branch-rate="0">
 					<methods/>
 					<lines>
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-						<line number="4" hits="1"/>
-						<line number="5" hits="1"/>
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 						<line number="47" hits="0"/>
 					</lines>
 				</class>
 			</classes>
 		</package>
-		<package name="data" line-rate="0.9065" branch-rate="0" complexity="0">
+		<package name="data" line-rate="0.7944" branch-rate="0" complexity="0">
 			<classes>
-				<class name="__init__.py" filename="data/__init__.py" complexity="0" line-rate="0.9101" branch-rate="0">
+				<class name="__init__.py" filename="data/__init__.py" complexity="0" line-rate="0.9551" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="6" hits="1"/>
@@ -2232,10 +2351,10 @@
 						<line number="100" hits="1"/>
 						<line number="101" hits="1"/>
 						<line number="103" hits="1"/>
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 						<line number="109" hits="1"/>
 						<line number="110" hits="1"/>
 						<line number="111" hits="1"/>
@@ -2262,47 +2381,47 @@
 						<line number="161" hits="1"/>
 					</lines>
 				</class>
-				<class name="__main__.py" filename="data/__main__.py" complexity="0" line-rate="0.8889" branch-rate="0">
+				<class name="__main__.py" filename="data/__main__.py" complexity="0" line-rate="0" branch-rate="0">
 					<methods/>
 					<lines>
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 						<line number="29" hits="0"/>
 					</lines>
 				</class>
 			</classes>
 		</package>
-		<package name="import_wrapper" line-rate="0.75" branch-rate="0" complexity="0">
+		<package name="import_wrapper" line-rate="0.15" branch-rate="0" complexity="0">
 			<classes>
 				<class name="__init__.py" filename="import_wrapper/__init__.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
 					<lines/>
 				</class>
-				<class name="helper.py" filename="import_wrapper/helper.py" complexity="0" line-rate="0.7" branch-rate="0">
+				<class name="helper.py" filename="import_wrapper/helper.py" complexity="0" line-rate="0" branch-rate="0">
 					<methods/>
 					<lines>
-						<line number="1" hits="1"/>
-						<line number="2" hits="1"/>
-						<line number="5" hits="1"/>
-						<line number="17" hits="1"/>
-						<line number="18" hits="1"/>
-						<line number="19" hits="1"/>
-						<line number="20" hits="1"/>
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+						<line number="2" hits="0"/>
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 						<line number="21" hits="0"/>
 						<line number="22" hits="0"/>
 						<line number="23" hits="0"/>
@@ -2318,21 +2437,21 @@
 						<line number="9" hits="1"/>
 					</lines>
 				</class>
-				<class name="typing.py" filename="import_wrapper/typing.py" complexity="0" line-rate="1" branch-rate="0">
+				<class name="typing.py" filename="import_wrapper/typing.py" complexity="0" line-rate="0" branch-rate="0">
 					<methods/>
 					<lines>
-						<line number="1" hits="1"/>
-						<line number="2" hits="1"/>
-						<line number="4" hits="1"/>
-						<line number="5" hits="1"/>
-						<line number="6" hits="1"/>
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+						<line number="4" hits="0"/>
+						<line number="5" hits="0"/>
+						<line number="6" hits="0"/>
 					</lines>
 				</class>
 			</classes>
 		</package>
-		<package name="tests" line-rate="0.9599" branch-rate="0" complexity="0">
+		<package name="tests" line-rate="0.8345" branch-rate="0" complexity="0">
 			<classes>
-				<class name="conftest.py" filename="tests/conftest.py" complexity="0" line-rate="0.875" branch-rate="0">
+				<class name="conftest.py" filename="tests/conftest.py" complexity="0" line-rate="0.375" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="1" hits="1"/>
@@ -2342,23 +2461,23 @@
 						<line number="6" hits="1"/>
 						<line number="9" hits="1"/>
 						<line number="12" hits="1"/>
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-						<line number="28" hits="1"/>
-						<line number="30" hits="1"/>
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 						<line number="32" hits="0"/>
 						<line number="33" hits="0"/>
 						<line number="34" hits="0"/>
-						<line number="40" hits="1"/>
+						<line number="40" hits="0"/>
 					</lines>
 				</class>
 				<class name="test_base_image.py" filename="tests/test_base_image.py" complexity="0" line-rate="0.96" branch-rate="0">
@@ -2391,43 +2510,6 @@
 						<line number="57" hits="0"/>
 					</lines>
 				</class>
-				<class name="test_config_cli.py" filename="tests/test_config_cli.py" complexity="0" line-rate="1" branch-rate="0">
-					<methods/>
-					<lines>
-						<line number="1" hits="1"/>
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-						<line number="28" hits="1"/>
-						<line number="29" hits="1"/>
-					</lines>
-				</class>
-				<class name="test_data_cli.py" filename="tests/test_data_cli.py" complexity="0" line-rate="1" branch-rate="0">
-					<methods/>
-					<lines>
-						<line number="1" hits="1"/>
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-						<line number="13" hits="1"/>
-						<line number="14" hits="1"/>
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-				</class>
 				<class name="test_images_tsv_results.py" filename="tests/test_images_tsv_results.py" complexity="0" line-rate="0.9412" branch-rate="0">
 					<methods/>
 					<lines>
@@ -2501,128 +2583,6 @@
 						<line number="145" hits="0"/>
 					</lines>
 				</class>
-				<class name="test_pipeline_cli.py" filename="tests/test_pipeline_cli.py" complexity="0" line-rate="1" branch-rate="0">
-					<methods/>
-					<lines>
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