diff --git a/lib/common.py b/lib/common.py
index 08959dc1..99abd398 100644
--- a/lib/common.py
+++ b/lib/common.py
@@ -27,6 +27,7 @@
     'merged_dir',
     'peaks_dir',
     'hub_config',
+    'include_references',
 ]
 
 
@@ -66,13 +67,17 @@ def resolve_config(config, workdir=None):
     if isinstance(config, str):
         config = yaml.load(open(config), Loader=yaml.FullLoader)
 
-    def rel(pth):
-        if workdir is None or os.path.isabs(pth):
+    def abs_path(pth):
+        if os.path.isabs(pth):
             return pth
         return os.path.join(workdir, pth)
     for key in PATH_KEYS:
-        if key in config:
-            config[key] = rel(config[key])
+        if key in config and workdir:
+            if isinstance(config[key], list):
+                for i in range(len(config[key])):
+                    config[key][i] = abs_path(config[key][i])
+            else:
+                config[key] = abs_path(config[key])
     return config
 
 
@@ -626,6 +631,10 @@ def load_config(config, missing_references_ok=False):
     handler.
     """
 
+    if isinstance(config, str):
+        config = yaml.load(open(config), Loader=yaml.FullLoader)
+
+    config = resolve_config(config)
     # Here we populate a list of reference sections. Items later on the list
     # will have higher priority
     includes = config.get('include_references', [])
diff --git a/lib/helpers.py b/lib/helpers.py
index 651a9c13..9a2b914e 100644
--- a/lib/helpers.py
+++ b/lib/helpers.py
@@ -219,7 +219,6 @@ def get_top_level_dir(start_dir=None):
         if current_dir == parent_dir:
             break
         current_dir = parent_dir
-        #TODO: Check for other edge cases?
 
-    return None
+    return current_dir
 
diff --git a/lib/patterns_targets.py b/lib/patterns_targets.py
index 542d4116..9a520b6b 100644
--- a/lib/patterns_targets.py
+++ b/lib/patterns_targets.py
@@ -9,6 +9,7 @@
 from . import common
 from . import chipseq
 from . import helpers
+from pathlib import Path
 
 HERE = os.path.abspath(os.path.dirname(__file__))
 
@@ -46,17 +47,17 @@ def __init__(self, config, patterns, workdir=None):
             as relative to `workdir`
         """
         self.path = None
-        self.workdir = '.'
+        self.workdir = None
         if workdir is not None:
-            config = os.path.join(workdir, config)
             patterns = os.path.join(workdir, patterns)
             self.workdir = workdir
 
         if isinstance(config, str):
+            config = os.path.join(workdir, config)
             self.path = config
 
         self.config = common.load_config(
-            common.resolve_config(config, workdir))
+            common.resolve_config(config, self.workdir))
 
         stranded = self.config.get('stranded', None)
         self.stranded = None
diff --git a/test/lcdb-wf-test b/test/lcdb-wf-test
index df59b24c..b6af4914 100755
--- a/test/lcdb-wf-test
+++ b/test/lcdb-wf-test
@@ -324,6 +324,7 @@ class Runner(object):
         if args.pytest:
             print_header("pytest")
             sp.run(["pytest", "--doctest-modules", "lib"], check=True, cwd=TOPLEVEL)
+            sp.run(["pytest", "test/tests"], check=True, cwd=TOPLEVEL)
 
         if args.url_check:
             print_header("url check")
diff --git a/test/tests/test_suite.py b/test/tests/test_suite.py
index b1389f03..3b7e9765 100644
--- a/test/tests/test_suite.py
+++ b/test/tests/test_suite.py
@@ -1,7 +1,8 @@
 import sys
+import os
 import subprocess
-top_level_dir = subprocess.run(["dirname $(dirname $(pwd))"], shell=True, capture_output=True, text=True).stdout.strip()
-print("top level dir: ", top_level_dir)
+from pathlib import Path
+top_level_dir = str(Path(".").resolve())
 sys.path.insert(0, top_level_dir)
 import pytest
 from textwrap import dedent
@@ -11,15 +12,15 @@
 @pytest.fixture
 def config(request):
     config_path = request.param
-    config = common.load_config(config_path, test=True)
-    return patterns_targets.RNASeqConfig(config, config.get('patterns', '../workflows/rnaseq/config/rnaseq_patterns.yaml'))
+    rnaseq_workdir = os.path.join(helpers.get_top_level_dir(), "workflows","rnaseq")
+    config = common.load_config(common.resolve_config(config_path, rnaseq_workdir))
+    return patterns_targets.RNASeqConfig(config, config.get('patterns', '../workflows/rnaseq/config/rnaseq_patterns.yaml'), workdir=rnaseq_workdir)
 
 # Call helpers.detect_layout(), which implicitly tests common.is_paired_end()
-# TODO: Make assertion condition NOT hard coded in to work with current example table
-@pytest.mark.parametrize("config", ['../../workflows/rnaseq/config/config.yaml'], indirect=True)
-def test_is_paired_end(config):
+@pytest.mark.parametrize("config, is_paired_ref", [("workflows/rnaseq/config/config.yaml", False)], indirect=["config"])
+def test_is_paired_end(config, is_paired_ref):
     is_paired = helpers.detect_layout(config.sampletable) == 'PE'
-    assert not is_paired, f"Test failed, is_paired = {is_paired}"
+    assert is_paired==is_paired_ref, f"Test failed, is_paired is {is_paired} when it should be {is_paired_ref}"
 
 def test_config_loading(tmpdir):
     f0 = tmpdir.mkdir('subdir').join('file0.yaml')