From 02e90763dc43e51b76c73f410c25961eedf2d899 Mon Sep 17 00:00:00 2001
From: Patricia Grubel <pagrubel@lanl.gov>
Date: Thu, 25 Sep 2025 15:53:39 -0600
Subject: [PATCH 1/8] Fix error for parsing workflow with and exception

---
 beeflow/client/bee_client.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/beeflow/client/bee_client.py b/beeflow/client/bee_client.py
index 9d0a4aa69..442758bcb 100644
--- a/beeflow/client/bee_client.py
+++ b/beeflow/client/bee_client.py
@@ -34,6 +34,7 @@
 from beeflow.common.connection import Connection
 from beeflow.common import paths
 from beeflow.common.parser import CwlParser
+from beeflow.common.parser.parser import CwlParseError
 from beeflow.common.object_models import generate_workflow_id
 from beeflow.client import core  # pylint: disable=R0401 #WIP
 from beeflow.client import remote_client
@@ -423,9 +424,15 @@ def is_parent(parent, path):
         yaml_path = untar_wf_path / pathlib.Path(yaml_file).name
         parser = CwlParser()
         workflow_id = generate_workflow_id()
-        workflow, tasks = parser.parse_workflow(
-            workflow_id, str(main_cwl_path), job=str(yaml_path), workdir=workdir
-        )
+        try:
+            workflow, tasks = parser.parse_workflow(
+                workflow_id, str(main_cwl_path), job=str(yaml_path), workdir=workdir
+            )
+
+        except CwlParseError as err:
+            print(f"{type(err).__name__}: {err}")
+            return None, []
+
         with open(package_path, "rb") as f:
             encoded_tarball = base64.b64encode(f.read()).decode("utf-8")
         shutil.rmtree(untar_path)
@@ -772,6 +779,7 @@ def reexecute(
     # Make sure the workdir is an absolute path and exists
     workdir = os.path.expanduser(workdir)
     workdir = os.path.abspath(workdir)
+
     if not os.path.exists(workdir):
         error_exit(f'Workflow working directory "{workdir}" doesn\'t exist')
     cwl_path = pathlib.Path(tempfile.mkdtemp())

From a9fd553ebaefb8029f88411b03091cff0f4badf8 Mon Sep 17 00:00:00 2001
From: Patricia Grubel <pagrubel@lanl.gov>
Date: Thu, 25 Sep 2025 15:54:56 -0600
Subject: [PATCH 2/8] Start on parsing pre and post scripts relative to the
 step/task workdir

---
 beeflow/common/parser/parser.py | 38 ++++++++++++++++++++++-----------
 1 file changed, 26 insertions(+), 12 deletions(-)

diff --git a/beeflow/common/parser/parser.py b/beeflow/common/parser/parser.py
index 9d0dae79d..5f5551299 100644
--- a/beeflow/common/parser/parser.py
+++ b/beeflow/common/parser/parser.py
@@ -131,8 +131,9 @@ def resolve_input(input_, type_):
             )
             for output in self.cwl.outputs
         ]
-        workflow_hints = self.parse_requirements(self.cwl.hints, as_hints=True)
-        workflow_requirements = self.parse_requirements(self.cwl.requirements)
+        print(f"Pat: workdir {workdir}")
+        workflow_hints = self.parse_requirements(self.cwl.hints, workdir, as_hints=True)
+        workflow_requirements = self.parse_requirements(self.cwl.requirements, workdir)
 
         workflow = Workflow(
             name=workflow_name,
@@ -179,10 +180,10 @@ def parse_step(self, step, workflow_id, workdir):
         step_name = os.path.basename(step_id).split(".")[0]
         step_command = step_cwl.baseCommand
         step_inputs = self.parse_step_inputs(step.in_, step_cwl.inputs)
-        step_requirements = self.parse_requirements(step.requirements)
-        step_requirements.extend(self.parse_requirements(step_cwl.requirements))
-        step_hints = self.parse_requirements(step.hints, as_hints=True)
-        step_hints.extend(self.parse_requirements(step_cwl.hints, as_hints=True))
+        step_requirements = self.parse_requirements(step.requirements, workdir)
+        step_requirements.extend(self.parse_requirements(step_cwl.requirements, workdir))
+        step_hints = self.parse_requirements(step.hints, workdir, as_hints=True)
+        step_hints.extend(self.parse_requirements(step_cwl.hints, workdir, as_hints=True))
         step_workdir = resolve_step_workdir(
             get_requirement(
                 step_requirements,
@@ -377,16 +378,24 @@ def parse_step_outputs(cwl_out, step_outputs, stdout, stderr, workdir=None):
             outputs.append(StepOutput(id=out, type=output_type, value=None, glob=glob))
         return outputs
 
-    def _read_requirement_file(self, key, items):
+    def _read_requirement_file(self, key, items, stepdir=None):
         """Read in a requirement file and replace it in the parsed items."""
-        base_path = os.path.dirname(self.path)
+        # pre and post scripts are relative to step workdir
+        if key in {"pre_script", "post_script"}:
+            if stepdir is None:
+                base_path = ""
+            else:
+                base_path = stepdir
+        else:
+            base_path = os.path.dirname(self.path)
         fname = items[key]
         path = os.path.join(base_path, fname)
+        print(f"Pat: path {path}")
         try:
             with open(path, encoding="utf-8") as fp:
                 items[key] = fp.read()
         except FileNotFoundError:
-            msg = f"Could not find a file for {key}: {fname}"
+            msg = f"Could not find a file for {key}: {path}"
             raise CwlParseError(msg) from None
         if key in {"pre_script", "post_script"}:
             self._validate_prepost_shell_env(key, items, fname)
@@ -418,7 +427,7 @@ def _validate_prepost_shell_env(self, key, items, fname):
         rm_line = "\n".join(rm_line)
         items.update({key: rm_line})
 
-    def parse_requirements(self, requirements, as_hints=False):
+    def parse_requirements(self, requirements, workdir, as_hints=False):
         """Parse CWL hints/requirements.
 
         :param requirements: the CWL requirements
@@ -428,9 +437,14 @@ def parse_requirements(self, requirements, as_hints=False):
         :rtype: list of Hint or list of Requirement or None
         """
         reqs = []
+        print(f"Pat: workdir {workdir}")
         if not requirements:
             return reqs
         if as_hints:
+            # The pre and post scripts are relative to the working directory for the step
+            stepdir = next((req["workdir"] for req in requirements if "workdir" in req), None)
+            if stepdir: stepdir = os.path.expanduser(stepdir)
+# I need to add the workdir/stepdir but what if it is an absolute path
             for req in requirements:
                 items = {}
                 for k, v in req.items():
@@ -445,7 +459,7 @@ def parse_requirements(self, requirements, as_hints=False):
                 # Load in pre/post scripts and make sure shell option is defined in cwl file
                 if "pre_script" in items and items["enabled"]:
                     if "shell" in items:
-                        self._read_requirement_file("pre_script", items)
+                        self._read_requirement_file("pre_script", items, stepdir=stepdir)
                     else:
                         msg = (
                             "pre script enabled but shell option undefined in cwl file."
@@ -453,7 +467,7 @@ def parse_requirements(self, requirements, as_hints=False):
                         raise CwlParseError(msg) from None
                 if "post_script" in items and items["enabled"]:
                     if "shell" in items:
-                        self._read_requirement_file("post_script", items)
+                        self._read_requirement_file("post_script", items, stepdir=stepdir)
                     else:
                         msg = "post script enabled but shell option undefined in cwl file."
                         raise CwlParseError(msg) from None

From d02d31a4291f4f968913801e4d0ee436db9370bf Mon Sep 17 00:00:00 2001
From: Patricia Grubel <pagrubel@lanl.gov>
Date: Mon, 20 Oct 2025 20:38:40 -0600
Subject: [PATCH 3/8] Remove debug statements

---
 beeflow/common/parser/parser.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/beeflow/common/parser/parser.py b/beeflow/common/parser/parser.py
index 5f5551299..4be9999f9 100644
--- a/beeflow/common/parser/parser.py
+++ b/beeflow/common/parser/parser.py
@@ -131,7 +131,6 @@ def resolve_input(input_, type_):
             )
             for output in self.cwl.outputs
         ]
-        print(f"Pat: workdir {workdir}")
         workflow_hints = self.parse_requirements(self.cwl.hints, workdir, as_hints=True)
         workflow_requirements = self.parse_requirements(self.cwl.requirements, workdir)
 
@@ -390,7 +389,6 @@ def _read_requirement_file(self, key, items, stepdir=None):
             base_path = os.path.dirname(self.path)
         fname = items[key]
         path = os.path.join(base_path, fname)
-        print(f"Pat: path {path}")
         try:
             with open(path, encoding="utf-8") as fp:
                 items[key] = fp.read()
@@ -437,7 +435,6 @@ def parse_requirements(self, requirements, workdir, as_hints=False):
         :rtype: list of Hint or list of Requirement or None
         """
         reqs = []
-        print(f"Pat: workdir {workdir}")
         if not requirements:
             return reqs
         if as_hints:

From c76030a988840d31f89191c4d356dd32c0fe39df Mon Sep 17 00:00:00 2001
From: Patricia Grubel <pagrubel@lanl.gov>
Date: Tue, 21 Oct 2025 13:43:57 -0600
Subject: [PATCH 4/8] Fix the scripts to work from workdir if no stepdir is
 specified and added documentation

---
 beeflow/client/bee_client.py    | 10 ++++------
 beeflow/common/parser/parser.py | 19 ++++++++++---------
 docs/sphinx/bee_cwl.rst         | 13 +++++++------
 3 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/beeflow/client/bee_client.py b/beeflow/client/bee_client.py
index 9d4bf910b..14733dfd0 100644
--- a/beeflow/client/bee_client.py
+++ b/beeflow/client/bee_client.py
@@ -33,7 +33,7 @@
 from beeflow.common.cli import NaturalOrderGroup
 from beeflow.common.connection import Connection
 from beeflow.common import paths
-from beeflow.common.parser import CwlParser
+from beeflow.common.parser import CwlParser # pylint: disable=C0415 # Costly import
 from beeflow.common.parser.parser import CwlParseError
 from beeflow.common.object_models import generate_workflow_id
 from beeflow.client import remote_client
@@ -366,12 +366,9 @@ def is_parent(parent, path):
     wf_path = wf_path.resolve()
     workdir = workdir.resolve()
 
-    # Make sure the workdir is an absolute path and exists
+    # Make sure the workdir is an absolute path
     workdir = os.path.expanduser(workdir)
     workdir = os.path.abspath(workdir)
-    if not os.path.exists(workdir):
-        error_exit(f'Workflow working directory "{workdir}" doesn\'t exist')
-
     # Make sure the workdir is not in /var or /var/tmp
     if os.path.commonpath([os.path.realpath("/tmp"), workdir]) == os.path.realpath(
         "/tmp"
@@ -382,6 +379,8 @@ def is_parent(parent, path):
     ):
         error_exit('Workflow working directory cannot be in "/var/tmp"')
 
+    # Create workdir if it does not exist
+    os.makedirs(workdir, exist_ok=True)
     tarball_path = ""
     workflow = None
     encoded_tarball = None
@@ -422,7 +421,6 @@ def is_parent(parent, path):
         main_cwl_path = untar_wf_path / pathlib.Path(main_cwl).name
         yaml_path = untar_wf_path / pathlib.Path(yaml_file).name
 
-        from beeflow.common.parser import CwlParser # pylint: disable=C0415 # Costly import
         parser = CwlParser()
         workflow_id = generate_workflow_id()
         try:
diff --git a/beeflow/common/parser/parser.py b/beeflow/common/parser/parser.py
index 4be9999f9..35d7ddc91 100644
--- a/beeflow/common/parser/parser.py
+++ b/beeflow/common/parser/parser.py
@@ -377,12 +377,13 @@ def parse_step_outputs(cwl_out, step_outputs, stdout, stderr, workdir=None):
             outputs.append(StepOutput(id=out, type=output_type, value=None, glob=glob))
         return outputs
 
-    def _read_requirement_file(self, key, items, stepdir=None):
+    def _read_requirement_file(self, key, items, workdir, stepdir=None):
         """Read in a requirement file and replace it in the parsed items."""
-        # pre and post scripts are relative to step workdir
+        # pre and post scripts are relative to the step workdir
+        # if step workdir is not not absolute then use workdir/stepdir
         if key in {"pre_script", "post_script"}:
             if stepdir is None:
-                base_path = ""
+                base_path = workdir
             else:
                 base_path = stepdir
         else:
@@ -440,8 +441,8 @@ def parse_requirements(self, requirements, workdir, as_hints=False):
         if as_hints:
             # The pre and post scripts are relative to the working directory for the step
             stepdir = next((req["workdir"] for req in requirements if "workdir" in req), None)
-            if stepdir: stepdir = os.path.expanduser(stepdir)
-# I need to add the workdir/stepdir but what if it is an absolute path
+            if stepdir:
+                stepdir = os.path.expanduser(stepdir)
             for req in requirements:
                 items = {}
                 for k, v in req.items():
@@ -452,11 +453,11 @@ def parse_requirements(self, requirements, workdir, as_hints=False):
                             items[k] = str(v)
                 # Load in the dockerfile at parse time
                 if "dockerFile" in items:
-                    self._read_requirement_file("dockerFile", items)
+                    self._read_requirement_file("dockerFile", items, workdir)
                 # Load in pre/post scripts and make sure shell option is defined in cwl file
                 if "pre_script" in items and items["enabled"]:
                     if "shell" in items:
-                        self._read_requirement_file("pre_script", items, stepdir=stepdir)
+                        self._read_requirement_file("pre_script", items, workdir, stepdir=stepdir)
                     else:
                         msg = (
                             "pre script enabled but shell option undefined in cwl file."
@@ -464,12 +465,12 @@ def parse_requirements(self, requirements, workdir, as_hints=False):
                         raise CwlParseError(msg) from None
                 if "post_script" in items and items["enabled"]:
                     if "shell" in items:
-                        self._read_requirement_file("post_script", items, stepdir=stepdir)
+                        self._read_requirement_file("post_script", items, workdir, stepdir=stepdir)
                     else:
                         msg = "post script enabled but shell option undefined in cwl file."
                         raise CwlParseError(msg) from None
                 if "beeflow:bindMounts" in items:
-                    self._read_requirement_file("beeflow:bindMounts", items)
+                    self._read_requirement_file("beeflow:bindMounts", items, workdir)
                 reqs.append(Hint(class_=req["class"], params=items))
         else:
             for req in requirements:
diff --git a/docs/sphinx/bee_cwl.rst b/docs/sphinx/bee_cwl.rst
index 445e7e222..27f719dbd 100644
--- a/docs/sphinx/bee_cwl.rst
+++ b/docs/sphinx/bee_cwl.rst
@@ -267,20 +267,21 @@ Some tasks may require small additional commands for setup or teardown such as
 loading modules, setting up checkpointing files, perserving outputs of subtasks
 that have been restarted, or cleaning up after a run.
 The script requirement enables this by adding shell scripts that will run before
-and after a task. The script must be within the workflow directory. The desired
+and after a task.  The desired
 shell interpreter must be specified in both the ``beeflow:ScriptRequirement`` section
 of the cwl file as well as the shebang line of the script, otherwise, an error will be
 returned. Furthermore, if different shell interpreters are specified, then expect
-an error. Default shell environment variable is ``/bin/bash``. The pre_script is run 
-before a task and the post_script is run after. Currently, we only support running 
-scripts outside of a container. We are considering adding container support in the 
+an error. Default shell environment variable is ``/bin/bash``. The pre_script is run
+before a task and the post_script is run after. Currently, we only support running
+scripts outside of a container. We are considering adding container support in the
 future.
+The scripts are assumed to be relative to the task working directory unless specified with an absolute path.
 
 ScriptRequirement currently supports the following options:
 
 * ``enabled`` - Enables pre/post script support
-* ``pre_script`` - Path to the pre_script relative to the workflow directory. 
-* ``post_script`` - Path to the post_script relative to the workflow directory.
+* ``pre_script`` - Path to the pre_script relative to the step working directory or specified absolute path.
+* ``post_script`` - Path to the post_script relative to the step working directory or specified absolute path.
 * ``shell`` - Desired shell interpreter. Must match shell interpreter defined in pre/post scripts.
 
 An example ``beeflow:ScriptRequirement`` is shown below::

From 6f8d3c316cd1a712f6e5d10e0978fd225f821b7a Mon Sep 17 00:00:00 2001
From: Patricia Grubel <pagrubel@lanl.gov>
Date: Wed, 22 Oct 2025 09:59:11 -0600
Subject: [PATCH 5/8] Add updating pip for python enviroment in documentation

---
 docs/sphinx/development.rst | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/docs/sphinx/development.rst b/docs/sphinx/development.rst
index f772bcb0b..e386a78a9 100644
--- a/docs/sphinx/development.rst
+++ b/docs/sphinx/development.rst
@@ -18,19 +18,20 @@ Additional Poetry documentation:
 Requirement: Python version 3.8 or greater
 ------------------------------------------
 
-Installation Using a Python Environment 
+Installation Using a Python Environment
 ---------------------------------------
 To install Poetry using a python environment, you must first set up the environment using the following
-commands (Please note that the name of the environment is not limited to beedev-env). 
+commands (Please note that the name of the environment is not limited to beedev-env).
 
 Please note the following instructions are intended for the Bash shell. If your default shell is Zsh,
-the instructions may be slightly different.        
+the instructions may be slightly different.
 
 .. code-block::
 
     mkdir beedev-env
     python3 -m venv beedev-env
-    source beedev-env/bin/activate 
+    source beedev-env/bin/activate
+    pip install --upgrade pip
     pip install poetry
 
 You can make sure Poetry is installed by using the following command: ``poetry --version``.

From 24297e433c67dc0e9ad9e9cb64e59f63104ca5d9 Mon Sep 17 00:00:00 2001
From: Patricia Grubel <pagrubel@lanl.gov>
Date: Tue, 28 Oct 2025 11:59:33 -0600
Subject: [PATCH 6/8] Fix if script path uses ~ for home directory

---
 beeflow/common/parser/parser.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/beeflow/common/parser/parser.py b/beeflow/common/parser/parser.py
index 35d7ddc91..d3fe9c84c 100644
--- a/beeflow/common/parser/parser.py
+++ b/beeflow/common/parser/parser.py
@@ -389,7 +389,13 @@ def _read_requirement_file(self, key, items, workdir, stepdir=None):
         else:
             base_path = os.path.dirname(self.path)
         fname = items[key]
-        path = os.path.join(base_path, fname)
+        fpath = Path(fname)
+        if fname.startswith("~"):
+            fpath = fpath.expanduser()
+        if fpath.is_absolute():
+            path = fpath
+        else:
+            path = os.path.join(base_path, fpath)
         try:
             with open(path, encoding="utf-8") as fp:
                 items[key] = fp.read()

From f1fda8bba81da8b0d400eda5f440ac8675d00e8a Mon Sep 17 00:00:00 2001
From: Patricia Grubel <pagrubel@lanl.gov>
Date: Tue, 28 Oct 2025 12:48:50 -0600
Subject: [PATCH 7/8] attempt fix for unit test

---
 beeflow/tests/test_parser.py              | 16 ++++++++++------
 ci/test_workflows/pre-post-script/post.sh |  3 ++-
 ci/test_workflows/pre-post-script/pre.sh  |  2 +-
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/beeflow/tests/test_parser.py b/beeflow/tests/test_parser.py
index e541d1028..c97f2edbd 100644
--- a/beeflow/tests/test_parser.py
+++ b/beeflow/tests/test_parser.py
@@ -52,8 +52,8 @@ def test_parse_workflow_yaml(self):
 
     def test_parse_workflow_script(self):
         """Test parsing of workflow with a YAML input job file."""
-        cwl_wf_file = find("beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/clamr_wf.cwl") # pylint: disable=C0301
-        cwl_job_yaml = find("beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/clamr_job.yml") # pylint: disable=C0301
+        cwl_wf_file = find("ci/test_workflows/pre-post-script/workflow.cwl") # pylint: disable=C0301
+        cwl_job_yaml = find("ci/test_workflows/pre-post-script/input.yml") # pylint: disable=C0301
 
         workflow_id = generate_workflow_id()
 
@@ -77,7 +77,7 @@ def test_parse_workflow_validate_script(self):
         self.assertEqual(context.exception.args[0], "No shebang line found in pre_run.sh")
 
     def test_parse_workflow_validate_shell(self):
-        """Test parsing of workflow and check shell option matches pre/post script shebang line."""
+        """Test parsing of workflow and check shell option pre/post script shebang line."""
         cwl_wf_file = find("ci/test_workflows/shell_validate/workflow.cwl")
         cwl_job_yaml = find("ci/test_workflows/shell_validate/input.yml")
 
@@ -86,7 +86,10 @@ def test_parse_workflow_validate_shell(self):
         with self.assertRaises(Exception) as context:
             self.parser.parse_workflow(workflow_id, cwl_wf_file, cwl_job_yaml)
 
-        self.assertEqual(context.exception.args[0], "CWL file shell #!/bin/bash does not match post.sh shell #!/bin/bashoo") # pylint: disable=C0301
+        self.assertEqual(
+            context.exception.args[0],
+            "CWL file shell #!/bin/bash does not match post.sh shell #!/bin/bash",
+        )
 
     def test_parse_workflow_json(self):
         """Test parsing of workflow with a JSON input job file."""
@@ -439,10 +442,11 @@ def test_parse_workflow_missing_input(self):
         ),
     ],
 )
-def test_parse_requirements_hints(requirements, exp_reqs):
+def test_parse_requirements_hints(requirements, workdir, exp_reqs):
     """Regression test parse_requirements when as_hints=True."""
     parser = CwlParser()
-    reqs = parser.parse_requirements(requirements, as_hints=True)
+    print(f"Pat: workdir {workdir}")
+    reqs = parser.parse_requirements(requirements, workdir, as_hints=True)
     assert reqs == exp_reqs
 
 
diff --git a/ci/test_workflows/pre-post-script/post.sh b/ci/test_workflows/pre-post-script/post.sh
index 550a41cfb..4acc63abf 100644
--- a/ci/test_workflows/pre-post-script/post.sh
+++ b/ci/test_workflows/pre-post-script/post.sh
@@ -1,3 +1,4 @@
 #!/bin/bash
-
 touch post.txt
+
+
diff --git a/ci/test_workflows/pre-post-script/pre.sh b/ci/test_workflows/pre-post-script/pre.sh
index 877699f60..d16281df1 100644
--- a/ci/test_workflows/pre-post-script/pre.sh
+++ b/ci/test_workflows/pre-post-script/pre.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
-
 touch pre.txt
+

From 600c536153bca3d84f8c6170ba0a8793555ad628 Mon Sep 17 00:00:00 2001
From: Patricia Grubel <pagrubel@lanl.gov>
Date: Tue, 28 Oct 2025 14:12:15 -0600
Subject: [PATCH 8/8] Fix unit tests

---
 beeflow/tests/test_parser.py                  |  9 +++--
 .../pre-post-script-validate/input.yml        |  1 +
 .../pre-post-script-validate/post.sh          |  3 ++
 .../pre-post-script-validate/pre.sh           |  1 +
 .../pre-post-script-validate/workflow.cwl     | 34 +++++++++++++++++++
 ci/test_workflows/pre-post-script/pre.sh      |  2 +-
 .../pre-post-script/workflow.cwl              |  4 +--
 ci/test_workflows/shell_validate/workflow.cwl |  4 +--
 8 files changed, 48 insertions(+), 10 deletions(-)
 create mode 100644 ci/test_workflows/pre-post-script-validate/input.yml
 create mode 100644 ci/test_workflows/pre-post-script-validate/post.sh
 create mode 100644 ci/test_workflows/pre-post-script-validate/pre.sh
 create mode 100644 ci/test_workflows/pre-post-script-validate/workflow.cwl

diff --git a/beeflow/tests/test_parser.py b/beeflow/tests/test_parser.py
index c97f2edbd..591cd3919 100644
--- a/beeflow/tests/test_parser.py
+++ b/beeflow/tests/test_parser.py
@@ -52,8 +52,8 @@ def test_parse_workflow_yaml(self):
 
     def test_parse_workflow_script(self):
         """Test parsing of workflow with a YAML input job file."""
-        cwl_wf_file = find("ci/test_workflows/pre-post-script/workflow.cwl") # pylint: disable=C0301
-        cwl_job_yaml = find("ci/test_workflows/pre-post-script/input.yml") # pylint: disable=C0301
+        cwl_wf_file = find("ci/test_workflows/pre-post-script/workflow.cwl")
+        cwl_job_yaml = find("ci/test_workflows/pre-post-script/input.yml")
 
         workflow_id = generate_workflow_id()
 
@@ -66,8 +66,8 @@ def test_parse_workflow_script(self):
 
     def test_parse_workflow_validate_script(self):
         """Test parsing of workflow and validate pre/post script files."""
-        cwl_wf_file = find("beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_wf.cwl") # pylint: disable=C0301
-        cwl_job_yaml = find("beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_job.yml") # pylint: disable=C0301
+        cwl_wf_file = find("ci/test_workflows/pre-post-script-validate/workflow.cwl")
+        cwl_job_yaml = find("ci/test_workflows/pre-post-script-validate/input.yml")
 
         workflow_id = generate_workflow_id()
 
@@ -445,7 +445,6 @@ def test_parse_workflow_missing_input(self):
 def test_parse_requirements_hints(requirements, workdir, exp_reqs):
     """Regression test parse_requirements when as_hints=True."""
     parser = CwlParser()
-    print(f"Pat: workdir {workdir}")
     reqs = parser.parse_requirements(requirements, workdir, as_hints=True)
     assert reqs == exp_reqs
 
diff --git a/ci/test_workflows/pre-post-script-validate/input.yml b/ci/test_workflows/pre-post-script-validate/input.yml
new file mode 100644
index 000000000..eaf9dc0e3
--- /dev/null
+++ b/ci/test_workflows/pre-post-script-validate/input.yml
@@ -0,0 +1 @@
+sleep_time: 1
diff --git a/ci/test_workflows/pre-post-script-validate/post.sh b/ci/test_workflows/pre-post-script-validate/post.sh
new file mode 100644
index 000000000..3322f2820
--- /dev/null
+++ b/ci/test_workflows/pre-post-script-validate/post.sh
@@ -0,0 +1,3 @@
+touch post.txt
+
+
diff --git a/ci/test_workflows/pre-post-script-validate/pre.sh b/ci/test_workflows/pre-post-script-validate/pre.sh
new file mode 100644
index 000000000..139e9084a
--- /dev/null
+++ b/ci/test_workflows/pre-post-script-validate/pre.sh
@@ -0,0 +1 @@
+touch pre.txt
diff --git a/ci/test_workflows/pre-post-script-validate/workflow.cwl b/ci/test_workflows/pre-post-script-validate/workflow.cwl
new file mode 100644
index 000000000..392548ebb
--- /dev/null
+++ b/ci/test_workflows/pre-post-script-validate/workflow.cwl
@@ -0,0 +1,34 @@
+class: Workflow
+cwlVersion: v1.0
+
+inputs:
+  sleep_time: int
+
+outputs:
+  step0_stdout:
+    type: File
+    outputSource: step0/step0_stdout
+
+steps:
+  step0:
+    run:
+      class: CommandLineTool
+      baseCommand: sleep
+      stdout: step0_stdout.txt
+      inputs:
+        sleep_time:
+          type: int
+          inputBinding:
+            position: 0
+      outputs:
+        step0_stdout:
+          type: stdout
+    in:
+      sleep_time: sleep_time
+    out: [step0_stdout]
+    hints:
+      beeflow:ScriptRequirement:
+        enabled: true
+        pre_script: "ci/test_workflows/pre-post-script/pre.sh"
+        post_script: "ci/test_workflows/pre-post-script/post.sh"
+        shell: "/bin/bash"
diff --git a/ci/test_workflows/pre-post-script/pre.sh b/ci/test_workflows/pre-post-script/pre.sh
index d16281df1..877699f60 100644
--- a/ci/test_workflows/pre-post-script/pre.sh
+++ b/ci/test_workflows/pre-post-script/pre.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
-touch pre.txt
 
+touch pre.txt
diff --git a/ci/test_workflows/pre-post-script/workflow.cwl b/ci/test_workflows/pre-post-script/workflow.cwl
index e1661a9c7..392548ebb 100644
--- a/ci/test_workflows/pre-post-script/workflow.cwl
+++ b/ci/test_workflows/pre-post-script/workflow.cwl
@@ -29,6 +29,6 @@ steps:
     hints:
       beeflow:ScriptRequirement:
         enabled: true
-        pre_script: "pre.sh"
-        post_script: "post.sh"
+        pre_script: "ci/test_workflows/pre-post-script/pre.sh"
+        post_script: "ci/test_workflows/pre-post-script/post.sh"
         shell: "/bin/bash"
diff --git a/ci/test_workflows/shell_validate/workflow.cwl b/ci/test_workflows/shell_validate/workflow.cwl
index e1661a9c7..392548ebb 100644
--- a/ci/test_workflows/shell_validate/workflow.cwl
+++ b/ci/test_workflows/shell_validate/workflow.cwl
@@ -29,6 +29,6 @@ steps:
     hints:
       beeflow:ScriptRequirement:
         enabled: true
-        pre_script: "pre.sh"
-        post_script: "post.sh"
+        pre_script: "ci/test_workflows/pre-post-script/pre.sh"
+        post_script: "ci/test_workflows/pre-post-script/post.sh"
         shell: "/bin/bash"