diff --git a/pkgs/by-name/cw/cwltool/package.nix b/pkgs/by-name/cw/cwltool/package.nix
index 15f387b7e131..57cf3be6963c 100644
--- a/pkgs/by-name/cw/cwltool/package.nix
+++ b/pkgs/by-name/cw/cwltool/package.nix
@@ -25,14 +25,14 @@ with py.pkgs;
 
 py.pkgs.buildPythonApplication rec {
   pname = "cwltool";
-  version = "3.1.20241217163858";
+  version = "3.1.20250110105449";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "common-workflow-language";
     repo = "cwltool";
     tag = version;
-    hash = "sha256-46x/7ewnt1eTu+1GdmPUExpiFfYE3mN8N8VFMM4r1Vk=";
+    hash = "sha256-V0CQiNkIw81s6e9224qcfbsOqBvMo34q+lRURpRetKs=";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/cwl-utils/default.nix b/pkgs/development/python-modules/cwl-utils/default.nix
index bc8ee3baf3e5..7fe9475b469e 100644
--- a/pkgs/development/python-modules/cwl-utils/default.nix
+++ b/pkgs/development/python-modules/cwl-utils/default.nix
@@ -4,6 +4,7 @@
   cwl-upgrader,
   cwlformat,
   fetchFromGitHub,
+  jsonschema,
   packaging,
   pytest-mock,
   pytest-xdist,
@@ -18,7 +19,7 @@
 
 buildPythonPackage rec {
   pname = "cwl-utils";
-  version = "0.36";
+  version = "0.37";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -27,7 +28,7 @@ buildPythonPackage rec {
     owner = "common-workflow-language";
     repo = "cwl-utils";
     tag = "v${version}";
-    hash = "sha256-ZSRwkZkBZ2cM0ZBvyI628xjbiho2FuFJnCYDZl3IrHs=";
+    hash = "sha256-OD8Nz8SIqB0Ie3S5663sQg3GjlCkC+qBvOXM9HZNuQU=";
   };
 
   build-system = [ setuptools ];
@@ -43,6 +44,7 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     cwlformat
+    jsonschema
     pytest-mock
     pytest-xdist
     pytestCheckHook
@@ -60,6 +62,7 @@ buildPythonPackage rec {
     # Don't run tests which require network access
     "test_remote_packing"
     "test_remote_packing_github_soft_links"
+    "test_cwl_inputs_to_jsonschema"
   ];
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/schema-salad/default.nix b/pkgs/development/python-modules/schema-salad/default.nix
index 736c77f9c133..019a86f9a05e 100644
--- a/pkgs/development/python-modules/schema-salad/default.nix
+++ b/pkgs/development/python-modules/schema-salad/default.nix
@@ -22,7 +22,7 @@
 
 buildPythonPackage rec {
   pname = "schema-salad";
-  version = "8.8.20241206093842";
+  version = "8.8.20250205075315";
   pyproject = true;
 
   disabled = pythonOlder "3.9";
@@ -31,12 +31,14 @@ buildPythonPackage rec {
     owner = "common-workflow-language";
     repo = "schema_salad";
     tag = version;
-    hash = "sha256-DUBrKBFphOa5hbEtsLVSI186TrhCkiNPtqlA61MENx0=";
+    hash = "sha256-Lev5daC3RCuXN1GJjOwplTx9PB3HTNZdNNzusn2dBaI=";
   };
 
+  pythonRelaxDeps = [ "mistune" ];
+
   postPatch = ''
     substituteInPlace pyproject.toml \
-      --replace-fail "mypy[mypyc]==1.13.0" "mypy"
+      --replace-fail "mypy[mypyc]==1.15.0" "mypy"
   '';
 
   build-system = [ setuptools-scm ];
@@ -65,6 +67,7 @@ buildPythonPackage rec {
 
   disabledTests = [
     "test_load_by_yaml_metaschema"
+    "test_detect_changes_in_html"
     # Setup for these tests requires network access
     "test_secondaryFiles"
     "test_outputBinding"