diff --git a/test/ci/codeclimate/codeclimate-clang-tidy/lib/runner.py b/test/ci/codeclimate/codeclimate-clang-tidy/lib/runner.py
index aa0b7ca47..b76464b74 100644
--- a/test/ci/codeclimate/codeclimate-clang-tidy/lib/runner.py
+++ b/test/ci/codeclimate/codeclimate-clang-tidy/lib/runner.py
@@ -1,106 +1,110 @@
 import json
 import subprocess
 import sys
 import re
 import tempfile
 
 from command import Command
 from issue_formatter import IssueFormatter
 from workspace import Workspace
 
 
 class Runner:
     CONFIG_FILE_PATH = '/config.json'
 
     """Runs clang-tidy, collects and reports results."""
     def __init__(self):
         self._config_file_path = self.CONFIG_FILE_PATH
-        #self._workspace_path = workspace_path
         pass
 
     def run(self):
         config = self._decode_config()
         self._print_debug(f'[clang-tidy] config: {config}')
 
         workspace = Workspace(config.get('include_paths'))
         workspace_files = workspace.calculate()
 
         if not len(workspace_files) > 0:
             return
 
         self._print_debug(f'[clang-tidy] analyzing {len(workspace_files)} files')
 
         plugin_config = config.get('config', {})
         command = Command(plugin_config, workspace_files).build()
 
-        command.append('src/')
         self._print_debug(f'[clang-tidy] command: {command}')
 
-        results = self._run_command(command)
-        issues = self._parse_results(results)
-
-        for issue in issues:
-            print(f'{json.dumps(issue)}\0')
+        issues = {}
+        for file_ in workspace_files:
+            results = self._run_command([*command, file_])
+            issues_ = self._parse_results(results)
+            issues.update(issues_)
+
+        for issue in issues.values():
+            # cppcheck will emit issues for files outside of the workspace,
+            # like header files. This ensures that we only emit issues for
+            # files in the workspace.
+            if issue and workspace.should_include(issue["location"]["path"]):
+                print('{}\0'.format(json.dumps(issue)))
 
     def _decode_config(self):
         self._print_debug(f"Decoding config file {self._config_file_path}")
 
         contents = ""
         with open(self._config_file_path, "r") as config:
             contents = config.read()
 
         return json.loads(contents)
 
     def _run_command(self, command):
         process = subprocess.Popen(command,
                                    stdout=subprocess.PIPE,
                                    stderr=subprocess.PIPE)
 
         stdout, stderr = process.communicate()
 
         return_vals = stdout.decode('utf-8').split('\n')
         return return_vals
 
     def _parse_results(self, results):
         ansi_escape = re.compile(r'''
         \x1B  # ESC
         (?:   # 7-bit C1 Fe (except CSI)
             [@-Z\\-_]
         |     # or [ for CSI, followed by a control sequence
             \[
             [0-?]*  # Parameter bytes
             [ -/]*  # Intermediate bytes
             [@-~]   # Final byte
         )''', re.VERBOSE)
 
         re_log_parse = re.compile(
             r'(?P<file>.*\.(cc|hh)):(?P<line>[0-9]+):(?P<column>[0-9]+): warning: (?P<detail>.*) \[(?P<type>.*)\]'  # noqa
         )
         issues = {}
         issue = None
 
         for line in results:
             clean_line = ansi_escape.sub('', line)
             match = re_log_parse.match(clean_line)
             if match:
                 if issue:
                     issue_ = IssueFormatter(issue).format()
                     issues[issue_['fingerprint']] = issue_
                 issue = match.groupdict()
             elif issue:
                 if 'content' in issue:
                     issue['content'].append(line)
                 else:
                     issue['content'] = [line]
             else:
                 issue = None
 
         if issue:
             issue_ = IssueFormatter(issue).format()
             issues[issue_['fingerprint']] = issue_
 
-        issues = list(issues.values())
         return issues
 
     def _print_debug(self, message):
         print(message, file=sys.stderr)