diff --git a/lib/extension.js b/lib/extension.js
index 3c9fde4..e0e015c 100644
--- a/lib/extension.js
+++ b/lib/extension.js
@@ -3,14 +3,17 @@ var fs = require('fs');
 var coverageHelpers = require('coverage-helpers');
 var coverageExclusions = [];
 
-function processor(resource, content) {
+function processor(resource, content, rootPath) {
+	if (typeof rootPath === 'undefined') {
+		rootPath = process.cwd();
+	}
     for (var i = 0; i < coverageExclusions.length; i++) {
         if (resource.path.indexOf(coverageExclusions[i]) !== -1) {
             return content;
         }
     }
     var contentBuffer = new Buffer(content, resource.encoding);
-    var fullPath = path.join(process.cwd(), resource.path);
+    var fullPath = path.join(rootPath, resource.path);
     return coverageHelpers.instrument(contentBuffer, fullPath).toString(resource.encoding);
 }
 
@@ -30,9 +33,14 @@ module.exports = {
 
     configure: function (config) {
         this.config_name = config.name;
+        if (typeof config.rootPath !== 'undefined') {
+			this.outputDirectory = path.join(config.rootPath, this.outputDirectory);
+		}
 
         config.on('load:sources', function (resourceSet) {
-            resourceSet.addProcessor(processor);
+            resourceSet.addProcessor(function (resource, content) {
+                return processor(resource, content, resourceSet.rootPath)
+            });
         });
 
         config.on('load:framework', function (resourceSet) {