diff --git a/lib/app.js b/lib/app.js
index 4e9e793..02bb1e7 100644
--- a/lib/app.js
+++ b/lib/app.js
@@ -104,7 +104,8 @@ class App {
           currentFile = file;
 
           const contractPath = path.resolve(file);
-          const canonicalPath = contractPath.split(this.coverageDir).join('');
+          const working = this.workingDir.substring(1);
+          const canonicalPath = contractPath.split('/coverageEnv').join(working);
           const contract = fs.readFileSync(contractPath).toString();
           const instrumentedContractInfo = getInstrumentedVersion(contract, canonicalPath);
           fs.writeFileSync(contractPath, instrumentedContractInfo.contract);
@@ -197,7 +198,7 @@ class App {
 
     return new Promise((resolve, reject) => {
       try {
-        this.coverage.generate(this.events, './contracts');
+        this.coverage.generate(this.events, `${this.workingDir}/contracts`);
 
         const json = JSON.stringify(this.coverage.coverage);
         fs.writeFileSync('./coverage.json', json);
diff --git a/test/app.js b/test/app.js
index e3a5706..6ec5c50 100644
--- a/test/app.js
+++ b/test/app.js
@@ -60,6 +60,7 @@ describe('app', () => {
       const testConfig = Object.assign({}, config);
 
       testConfig.testrpcOptions = `--account="${privateKey},${balance}" --port 8777`;
+      testConfig.dir = './mock',
       testConfig.norpc = false;
       testConfig.port = 8777;
 
@@ -78,6 +79,7 @@ describe('app', () => {
       const testConfig = Object.assign({}, config);
 
       testConfig.testCommand = 'mocha --timeout 5000 > /dev/null 2>&1';
+      testConfig.dir = './mock',
       testConfig.norpc = false;
       testConfig.port = 8888;
 
@@ -96,6 +98,7 @@ describe('app', () => {
       const testConfig = Object.assign({}, config);
 
       testConfig.testCommand = 'node ../test/util/mockTestCommand.js';
+      testConfig.dir = './mock',
       testConfig.norpc = false;
       testConfig.port = 8888;
 
@@ -115,6 +118,7 @@ describe('app', () => {
 
       const testConfig = Object.assign({}, config);
 
+      testConfig.dir = './mock',
       testConfig.norpc = false;
       testConfig.port = 8889;
 
@@ -155,6 +159,7 @@ describe('app', () => {
       };`;
 
       const testConfig = Object.assign({}, config);
+      testConfig.dir = './mock',
       testConfig.norpc = false;
       testConfig.port = 8555; // Manually inspect that port is actually set to 8999