diff --git a/packages/backend-common/src/util/docker.test.ts b/packages/backend-common/src/util/docker.test.ts
index 7f9bb2da33..8af6a7366f 100644
--- a/packages/backend-common/src/util/docker.test.ts
+++ b/packages/backend-common/src/util/docker.test.ts
@@ -14,15 +14,24 @@
  * limitations under the License.
  */
 import Docker from 'dockerode';
-import fs from 'fs';
+import mockFs from 'mock-fs';
 import os from 'os';
+import path from 'path';
 import Stream, { PassThrough } from 'stream';
 import { runDockerContainer, UserOptions } from './docker';
 
 const mockDocker = new Docker() as jest.Mocked<Docker>;
+const rootDir = os.platform() === 'win32' ? 'C:\\rootDir' : '/rootDir';
 
 describe('runDockerContainer', () => {
   beforeEach(() => {
+    mockFs({
+      [rootDir]: {
+        input: mockFs.directory(),
+        output: mockFs.directory(),
+      },
+    });
+
     jest.spyOn(mockDocker, 'pull').mockImplementation((async (
       _image: string,
       _something: any,
@@ -42,17 +51,23 @@ describe('runDockerContainer', () => {
       .mockResolvedValue(Buffer.from('OK', 'utf-8'));
   });
 
+  afterEach(() => {
+    mockFs.restore();
+  });
+
   const imageName = 'dockerOrg/image';
   const args = ['bash', '-c', 'echo test'];
-  const inputDir = os.tmpdir();
-  const outputDir = os.tmpdir();
+  const mountDirs = new Map([
+    [path.join(rootDir, 'input'), '/input'],
+    [path.join(rootDir, 'output'), '/output'],
+  ]);
+  const workingDir = path.join(rootDir, 'input');
+  const envVars = ['HOME=/tmp', 'LOG_LEVEL=debug'];
 
   it('should pull the docker container', async () => {
     await runDockerContainer({
       imageName,
       args,
-      inputDir,
-      outputDir,
       dockerClient: mockDocker,
     });
 
@@ -61,14 +76,17 @@ describe('runDockerContainer', () => {
       {},
       expect.any(Function),
     );
+
+    expect(mockDocker.run).toHaveBeenCalled();
   });
 
   it('should call the dockerClient run command with the correct arguments passed through', async () => {
     await runDockerContainer({
       imageName,
       args,
-      inputDir,
-      outputDir,
+      mountDirs,
+      envVars,
+      workingDir,
       dockerClient: mockDocker,
     });
 
@@ -77,10 +95,12 @@ describe('runDockerContainer', () => {
       args,
       expect.any(Stream),
       expect.objectContaining({
+        Env: envVars,
+        WorkingDir: workingDir,
         HostConfig: {
           Binds: expect.arrayContaining([
-            `${await fs.promises.realpath(inputDir)}:/input`,
-            `${await fs.promises.realpath(outputDir)}:/output`,
+            `${path.join(rootDir, 'input')}:/input`,
+            `${path.join(rootDir, 'output')}:/output`,
           ]),
         },
         Volumes: {
@@ -95,8 +115,6 @@ describe('runDockerContainer', () => {
     await runDockerContainer({
       imageName,
       args,
-      inputDir,
-      outputDir,
       dockerClient: mockDocker,
     });
 
@@ -107,8 +125,6 @@ describe('runDockerContainer', () => {
     await runDockerContainer({
       imageName,
       args,
-      inputDir,
-      outputDir,
       dockerClient: mockDocker,
     });
 
@@ -139,8 +155,6 @@ describe('runDockerContainer', () => {
       runDockerContainer({
         imageName,
         args,
-        inputDir,
-        outputDir,
         dockerClient: mockDocker,
       }),
     ).rejects.toThrow(/Something went wrong with docker/);
@@ -160,8 +174,6 @@ describe('runDockerContainer', () => {
         runDockerContainer({
           imageName,
           args,
-          inputDir,
-          outputDir,
           dockerClient: mockDocker,
         }),
       ).rejects.toThrow(new RegExp(`.+: ${dockerError}`));
@@ -173,8 +185,6 @@ describe('runDockerContainer', () => {
     await runDockerContainer({
       imageName,
       args,
-      inputDir,
-      outputDir,
       logStream,
       dockerClient: mockDocker,
     });
@@ -185,15 +195,9 @@ describe('runDockerContainer', () => {
       logStream,
       expect.objectContaining({
         HostConfig: {
-          Binds: expect.arrayContaining([
-            `${await fs.promises.realpath(inputDir)}:/input`,
-            `${await fs.promises.realpath(outputDir)}:/output`,
-          ]),
-        },
-        Volumes: {
-          '/input': {},
-          '/output': {},
+          Binds: [],
         },
+        Volumes: {},
       }),
     );
   });
diff --git a/packages/backend-common/src/util/docker.ts b/packages/backend-common/src/util/docker.ts
index 9d2bccd549..f2d1ff6993 100644
--- a/packages/backend-common/src/util/docker.ts
+++ b/packages/backend-common/src/util/docker.ts
@@ -15,7 +15,6 @@
  */
 
 import Docker from 'dockerode';
-import fs from 'fs';
 import { PassThrough, Writable } from 'stream';
 
 export type UserOptions = {
@@ -26,9 +25,10 @@ export type RunDockerContainerOptions = {
   imageName: string;
   args: string[];
   logStream?: Writable;
-  inputDir: string;
-  outputDir: string;
   dockerClient: Docker;
+  mountDirs?: Map<string, string>;
+  workingDir?: string;
+  envVars?: string[];
   createOptions?: Docker.ContainerCreateOptions;
 };
 
@@ -38,17 +38,20 @@ export type RunDockerContainerOptions = {
  * @param options.imageName the image to run
  * @param options.args the arguments to pass the container
  * @param options.logStream the log streamer to capture log messages
- * @param options.inputDir the /input path inside the container
- * @param options.outputDir the /output path inside the container
  * @param options.dockerClient the dockerClient to use
+ * @param options.mountDirs A map of host directories to mount on the container.
+ *        Map Key: Path on host machine, Value: Path on Docker container
+ * @param options.workingDir Working dir in the container
+ * @param options.envVars Environment variables to set in the container. e.g. ['HOME=/tmp']
  */
 export const runDockerContainer = async ({
   imageName,
   args,
   logStream = new PassThrough(),
-  inputDir,
-  outputDir,
   dockerClient,
+  mountDirs = new Map(),
+  workingDir,
+  envVars = [],
   createOptions = {},
 }: RunDockerContainerOptions) => {
   // Show a better error message when Docker is unavailable.
@@ -80,25 +83,30 @@ export const runDockerContainer = async ({
     userOptions.User = `${process.getuid()}:${process.getgid()}`;
   }
 
+  // Initialize volumes to mount based on mountDirs map
+  const Volumes: { [T: string]: object } = {};
+  for (const containerDir of mountDirs.values()) {
+    Volumes[containerDir] = {};
+  }
+
+  // Create bind volumes
+  const Binds: string[] = [];
+  for (const [hostDir, containerDir] of mountDirs.entries()) {
+    Binds.push(`${hostDir}:${containerDir}`);
+  }
+
   const [{ Error: error, StatusCode: statusCode }] = await dockerClient.run(
     imageName,
     args,
     logStream,
     {
-      Volumes: { '/output': {}, '/input': {} },
-      WorkingDir: '/input',
+      Volumes,
       HostConfig: {
-        Binds: [
-          // Need to use realpath here as Docker mounting does not like
-          // symlinks for binding volumes
-          `${await fs.promises.realpath(outputDir)}:/output`,
-          `${await fs.promises.realpath(inputDir)}:/input`,
-        ],
+        Binds,
       },
+      ...(workingDir ? { WorkingDir: workingDir } : {}),
+      Env: envVars,
       ...userOptions,
-      // Set the home directory inside the container as something that applications can
-      // write to, otherwise they will just flop and fail trying to write to /
-      Env: ['HOME=/tmp'],
       ...createOptions,
     },
   );