I was able to find out how to use AVAssetWriter. In case anyone else needs help the code I used is as follows:
func setUpWriter() {
    do {
        outputFileLocation = videoFileLocation()
        videoWriter = try AVAssetWriter(outputURL: outputFileLocation!, fileType: AVFileType.mov)
        // add video input
        videoWriterInput = AVAssetWriterInput(mediaType: AVMediaType.video, outputSettings: [
            AVVideoCodecKey : AVVideoCodecType.h264,
            AVVideoWidthKey : 720,
            AVVideoHeightKey : 1280,
            AVVideoCompressionPropertiesKey : [
                AVVideoAverageBitRateKey : 2300000,
                ],
            ])
        videoWriterInput.expectsMediaDataInRealTime = true
        if videoWriter.canAdd(videoWriterInput) {
            videoWriter.add(videoWriterInput)
            print("video input added")
        } else {
            print("no input added")
        }
        // add audio input
        audioWriterInput = AVAssetWriterInput(mediaType: AVMediaType.audio, outputSettings: nil)
        audioWriterInput.expectsMediaDataInRealTime = true
        if videoWriter.canAdd(audioWriterInput!) {
            videoWriter.add(audioWriterInput!)
            print("audio input added")
        }
        videoWriter.startWriting()
    } catch let error {
        debugPrint(error.localizedDescription)
    }
}
func canWrite() -> Bool {
    return isRecording && videoWriter != nil && videoWriter?.status == .writing
}
 //video file location method
func videoFileLocation() -> URL {
    let documentsPath = NSSearchPathForDirectoriesInDomains(.documentDirectory, .userDomainMask, true)[0] as NSString
    let videoOutputUrl = URL(fileURLWithPath: documentsPath.appendingPathComponent("videoFile")).appendingPathExtension("mov")
    do {
    if FileManager.default.fileExists(atPath: videoOutputUrl.path) {
        try FileManager.default.removeItem(at: videoOutputUrl)
        print("file removed")
    }
    } catch {
        print(error)
    }
    return videoOutputUrl
}
// MARK: AVCaptureVideoDataOutputSampleBufferDelegate
func captureOutput(_ output: AVCaptureOutput, didOutput sampleBuffer: CMSampleBuffer, from connection: AVCaptureConnection) {
    let writable = canWrite()
    if writable,
        sessionAtSourceTime == nil {
        // start writing
        sessionAtSourceTime = CMSampleBufferGetPresentationTimeStamp(sampleBuffer)
        videoWriter.startSession(atSourceTime: sessionAtSourceTime!)
        //print("Writing")
    }
    if output == videoDataOutput {
        connection.videoOrientation = .portrait
        if connection.isVideoMirroringSupported {
            connection.isVideoMirrored = true
        }
    }
    if writable,
        output == videoDataOutput,
        (videoWriterInput.isReadyForMoreMediaData) {
        // write video buffer
        videoWriterInput.append(sampleBuffer)
        //print("video buffering")
    } else if writable,
        output == audioDataOutput,
        (audioWriterInput.isReadyForMoreMediaData) {
        // write audio buffer
        audioWriterInput?.append(sampleBuffer)
        //print("audio buffering")
    }
}
// MARK: Start recording
func start() {
    guard !isRecording else { return }
    isRecording = true
    sessionAtSourceTime = nil
    setUpWriter()
    print(isRecording)
    print(videoWriter)
    if videoWriter.status == .writing {
        print("status writing")
    } else if videoWriter.status == .failed {
        print("status failed")
    } else if videoWriter.status == .cancelled {
        print("status cancelled")
    } else if videoWriter.status == .unknown {
        print("status unknown")
    } else {
        print("status completed")
    }
}
// MARK: Stop recording
func stop() {
    guard isRecording else { return }
    isRecording = false
    videoWriterInput.markAsFinished()
    print("marked as finished")
    videoWriter.finishWriting { [weak self] in
        self?.sessionAtSourceTime = nil
    }
    //print("finished writing \(self.outputFileLocation)")
    captureSession.stopRunning()
    performSegue(withIdentifier: "videoPreview", sender: nil)
}
I now have another problem where this solution doesn't work when I'm using AVCaptureMetadataOutput, AVCaptureVideoDataOutput and AVCaptureAudioDataOutput together. The app crashes when I add AVCaptureAudioDataOutput.