diff --git a/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix
new file mode 100644
index 000000000000..21e3c47b323d
--- /dev/null
+++ b/pkgs/applications/science/misc/cwltool/default.nix
@@ -0,0 +1,41 @@
+{ lib
+, python3Packages
+}:
+
+python3Packages.buildPythonApplication rec {
+  pname = "cwltool";
+  version = "3.1.20210628163208";
+
+  src = python3Packages.fetchPypi {
+    inherit pname version;
+    sha256 = "21b885f725420413d2f87eadc5e81c08a9c91beceda89b35d1a702ec4df47e52";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace 'prov == 1.5.1' 'prov'
+  '';
+
+  propagatedBuildInputs = with python3Packages; [
+    argcomplete
+    bagit
+    coloredlogs
+    mypy-extensions
+    prov
+    psutil
+    pydot
+    schema-salad
+    shellescape
+    typing-extensions
+  ];
+
+  doCheck = false; # hard to setup
+  pythonImportsCheck = [ "cwltool" ];
+
+  meta = with lib; {
+    homepage = "https://www.commonwl.org";
+    license = with licenses; [ asl20 ];
+    description = "Common Workflow Language reference implementation";
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index ed1329180b20..ec1c177e2c5b 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -13403,6 +13403,8 @@ in
     inherit (llvmPackages_11) llvm libclang;
   };
 
+  cwltool = callPackage ../applications/science/misc/cwltool { };
+
   dprint = callPackage ../development/tools/dprint { };
 
   libcxx = llvmPackages.libcxx;