diff --git a/pkgs/by-name/cw/cwltool/package.nix b/pkgs/by-name/cw/cwltool/package.nix
index 57cf3be6963c..6cde031522fc 100644
--- a/pkgs/by-name/cw/cwltool/package.nix
+++ b/pkgs/by-name/cw/cwltool/package.nix
@@ -40,6 +40,8 @@ py.pkgs.buildPythonApplication rec {
       --replace-fail "prov == 1.5.1" "prov" \
       --replace-fail '"schema-salad >= 8.7, < 9",' '"schema-salad",' \
       --replace-fail "PYTEST_RUNNER + " ""
+    substituteInPlace pyproject.toml \
+      --replace-fail "mypy==1.14.1" "mypy"
   '';
 
   build-system = with py.pkgs; [
diff --git a/pkgs/development/python-modules/cwl-utils/default.nix b/pkgs/development/python-modules/cwl-utils/default.nix
index 7fe9475b469e..2bb0a6444896 100644
--- a/pkgs/development/python-modules/cwl-utils/default.nix
+++ b/pkgs/development/python-modules/cwl-utils/default.nix
@@ -19,7 +19,7 @@
 
 buildPythonPackage rec {
   pname = "cwl-utils";
-  version = "0.37";
+  version = "0.38";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -28,7 +28,7 @@ buildPythonPackage rec {
     owner = "common-workflow-language";
     repo = "cwl-utils";
     tag = "v${version}";
-    hash = "sha256-OD8Nz8SIqB0Ie3S5663sQg3GjlCkC+qBvOXM9HZNuQU=";
+    hash = "sha256-goeMlyHYiS4JLOVBFjcLSzdYrdoIZ904hJHFPGZyxKo=";
   };
 
   build-system = [ setuptools ];
@@ -65,6 +65,15 @@ buildPythonPackage rec {
     "test_cwl_inputs_to_jsonschema"
   ];
 
+  disabledTestPaths = [
+    # Tests require podman
+    "tests/test_docker_extract.py"
+    # Tests requires singularity
+    "tests/test_js_sandbox.py"
+    # Circular dependencies
+    "tests/test_graph_split.py"
+  ];
+
   meta = with lib; {
     description = "Utilities for CWL";
     homepage = "https://github.com/common-workflow-language/cwl-utils";