diff --git a/.github/workflows/complete_release.yml b/.github/workflows/complete_release.yml
index cdb9fb93..0a0b30e3 100644
--- a/.github/workflows/complete_release.yml
+++ b/.github/workflows/complete_release.yml
@@ -37,12 +37,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: ./.github/actions/setup-bfabricpy
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.12
+      - name: Install nox
+        run: pip install nox uv
       - name: Publish documentation
         run: |
           set -euxo pipefail
           git fetch --unshallow origin gh-pages
           git checkout gh-pages && git pull && git checkout -
-          uv run mkdocs gh-deploy
+          nox -s docs
+          nox -s publish_docs
diff --git a/docs/changelog.md b/docs/changelog.md
index e08d67ad..1659f84d 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -10,6 +10,21 @@ Versioning currently follows `X.Y.Z` where
 
 ## \[Unreleased\]
 
+## \[1.13.10\] - 2024-12-13
+
+### Fixed
+
+- If `bfabricpy.yml` contains a root-level key which is not a dictionary, a correct error message is shown instead of raising an exception.
+- A bug introduced while refactoring in `slurm.py` which passed `Path` objects to `subprocess` instead of strings.
+- Submitter
+    - does not use unset `JOB_ID` environment variable anymore.
+    - does not set unused `STAMP` environment variable anymore.
+- Fix `bfabric_save_workflowstep.py` bugs from refactoring.
+
+### Added
+
+- Experimental bfabric-cli interface. Please do not use it in production yet as it will need a lot of refinement.
+
 ## \[1.13.9\] - 2024-12-10
 
 From this release onwards, the experimental app runner is not part of the main bfabric package and
diff --git a/pyproject.toml b/pyproject.toml
index 227aaef1..e80c546c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "bfabric"
 description = "Python client for the B-Fabric WSDL API"
-version = "1.13.9"
+version = "1.13.10"
 license = { text = "GPL-3.0" }
 authors = [
     { name = "Christian Panse", email = "cp@fgcz.ethz.ch" },
@@ -78,6 +78,8 @@ Repository = "https://github.com/fgcz/bfabricPy"
 "bfabric_slurm_queue_status.py" = "bfabric_scripts.bfabric_slurm_queue_status:main"
 "bfabric_save_resource_description.py" = "bfabric_scripts.bfabric_save_resource_description:main"
 
+"bfabric-cli" = "bfabric_scripts.cli.__main__:app"
+
 [tool.setuptools.package-data]
 "*" = ["py.typed"]
 
diff --git a/src/bfabric/config/config_file.py b/src/bfabric/config/config_file.py
index 1983ba9a..aeb93728 100644
--- a/src/bfabric/config/config_file.py
+++ b/src/bfabric/config/config_file.py
@@ -23,13 +23,15 @@ class EnvironmentConfig(BaseModel):
     @classmethod
     def gather_config(cls, values: dict[str, Any]) -> dict[str, Any]:
         """Gathers all configs into the config field."""
+        if not isinstance(values, dict):
+            return values
         values["config"] = {key: value for key, value in values.items() if key not in ["login", "password"]}
         return values
 
     @model_validator(mode="before")
     @classmethod
     def gather_auth(cls, values: dict[str, Any]) -> dict[str, Any]:
-        if "login" in values:
+        if isinstance(values, dict) and "login" in values:
             values["auth"] = BfabricAuth.model_validate(values)
         return values
 
diff --git a/src/bfabric/wrapper_creator/bfabric_submitter.py b/src/bfabric/wrapper_creator/bfabric_submitter.py
index 7ef35c1c..0e258b19 100644
--- a/src/bfabric/wrapper_creator/bfabric_submitter.py
+++ b/src/bfabric/wrapper_creator/bfabric_submitter.py
@@ -100,17 +100,10 @@ def compose_bash_script(self, configuration=None, configuration_parser=lambda x:
 #SBATCH -e {stderr_url}
 #SBATCH -o {stdout_url}
 #SBATCH --job-name=WU{workunit_id}
-#SBATCH --workdir=/home/bfabric
+#SBATCH --chdir=/home/bfabric
 #SBATCH --export=ALL,HOME=/home/bfabric
 
-# Grid Engine Parameters
-#$ -q {partition}&{nodelist}
-#$ -e {stderr_url}
-#$ -o {stdout_url}
-
-
-set -e
-set -o pipefail
+set -euxo pipefail
 
 export EMAIL="{job_notification_emails}"
 export EXTERNALJOB_ID={external_job_id}
@@ -118,7 +111,6 @@ def compose_bash_script(self, configuration=None, configuration_parser=lambda x:
 export RESSOURCEID_STDOUT_STDERR="{resource_id_stderr} {resource_id_stdout}"
 export OUTPUT="{output_list}"
 export WORKUNIT_ID="{workunit_id}"
-STAMP=`/bin/date +%Y%m%d%H%M`.$$.$JOB_ID
 TEMPDIR="/home/bfabric/prx"
 
 _OUTPUT=`echo $OUTPUT | cut -d"," -f1`
@@ -146,11 +138,11 @@ def compose_bash_script(self, configuration=None, configuration_parser=lambda x:
 ## interrupt here if you want to do a semi-automatic processing
 if [ -x /usr/bin/mutt ];
 then
-    cat $0 > $TEMPDIR/$JOB_ID.bash
+    cat $0 > $TEMPDIR/$EXTERNALJOB_ID.bash
 
     (who am i; hostname; uptime; echo $0; pwd; ps;) \
-    | mutt -s "JOB_ID=$JOB_ID WORKUNIT_ID=$WORKUNIT_ID EXTERNALJOB_ID=$EXTERNALJOB_ID" $EMAIL \
-        -a $TEMPDIR/$JOB_ID.bash $TEMPDIR/config_WU$WORKUNIT_ID.yaml
+    | mutt -s "WORKUNIT_ID=$WORKUNIT_ID EXTERNALJOB_ID=$EXTERNALJOB_ID" $EMAIL \
+        -a $TEMPDIR/$EXTERNALJOB_ID.bash $TEMPDIR/config_WU$WORKUNIT_ID.yaml
 fi
 # exit 0
 
@@ -161,7 +153,7 @@ def compose_bash_script(self, configuration=None, configuration_parser=lambda x:
 if [ $? -eq 0 ];
 then
      ssh fgcz-r-035.uzh.ch "bfabric_setResourceStatus_available.py $RESSOURCEID_OUTPUT" \
-     | mutt -s "JOB_ID=$JOB_ID WORKUNIT_ID=$WORKUNIT_ID EXTERNALJOB_ID=$EXTERNALJOB_ID DONE" $EMAIL
+     | mutt -s "WORKUNIT_ID=$WORKUNIT_ID EXTERNALJOB_ID=$EXTERNALJOB_ID DONE" $EMAIL
 
      bfabric_save_workflowstep.py $WORKUNIT_ID
      bfabric_setExternalJobStatus_done.py $EXTERNALJOB_ID
@@ -169,7 +161,7 @@ def compose_bash_script(self, configuration=None, configuration_parser=lambda x:
     echo $?
 else
     echo "application failed"
-     mutt -s "JOB_ID=$JOB_ID WORKUNIT_ID=$WORKUNIT_ID EXTERNALJOB_ID=$EXTERNALJOB_ID failed" $EMAIL < /dev/null
+     mutt -s "WORKUNIT_ID=$WORKUNIT_ID EXTERNALJOB_ID=$EXTERNALJOB_ID failed" $EMAIL < /dev/null
      bfabric_setResourceStatus_available.py $RESSOURCEID_STDOUT_STDERR $RESSOURCEID;
     exit 1;
 fi
diff --git a/src/bfabric/wrapper_creator/bfabric_wrapper_creator.py b/src/bfabric/wrapper_creator/bfabric_wrapper_creator.py
index e0e59959..8090b511 100644
--- a/src/bfabric/wrapper_creator/bfabric_wrapper_creator.py
+++ b/src/bfabric/wrapper_creator/bfabric_wrapper_creator.py
@@ -6,6 +6,7 @@
 from pathlib import Path
 from typing import Any, Literal
 
+import yaml
 from loguru import logger
 
 from bfabric import Bfabric
@@ -71,7 +72,7 @@ def create_log_resource(self, variant: Literal["out", "err"], output_resource: R
                 "name": f"slurm_std{variant}",
                 "workunitid": self.workunit_definition.registration.workunit_id,
                 "storageid": self._log_storage.id,
-                "relativepath": f"/workunitid-{self._workunit.id}_resourceid-{output_resource.id}.{variant}",
+                "relativepath": f"workunitid-{self._workunit.id}_resourceid-{output_resource.id}.{variant}",
             },
         )
         return Resource(result[0])
@@ -177,3 +178,19 @@ def write_results(self, config_serialized: str) -> tuple[dict[str, Any], dict[st
         self._client.save("externaljob", {"id": self._external_job_id, "status": "done"})
 
         return yaml_workunit_executable, yaml_workunit_externaljob
+
+    def create(self) -> tuple[dict[str, Any], dict[str, Any], dict[str, Any]]:
+        """Creates the YAML file external job and resources, and registers everything in B-Fabric."""
+        output_resource = self.create_output_resource()
+        stdout_resource = self.create_log_resource(variant="out", output_resource=output_resource)
+        stderr_resource = self.create_log_resource(variant="err", output_resource=output_resource)
+
+        config_dict = {
+            "application": self.get_application_section(output_resource=output_resource),
+            "job_configuration": self.get_job_configuration_section(
+                output_resource=output_resource, stdout_resource=stdout_resource, stderr_resource=stderr_resource
+            ),
+        }
+        config_serialized = yaml.safe_dump(config_dict)
+        yaml_workunit_executable, yaml_workunit_externaljob = self.write_results(config_serialized=config_serialized)
+        return config_dict, yaml_workunit_executable, yaml_workunit_externaljob
diff --git a/src/bfabric/wrapper_creator/slurm.py b/src/bfabric/wrapper_creator/slurm.py
index 2315b492..9f875f53 100644
--- a/src/bfabric/wrapper_creator/slurm.py
+++ b/src/bfabric/wrapper_creator/slurm.py
@@ -61,7 +61,12 @@ def sbatch(self, script: str | Path) -> tuple[str, str] | None:
 
         env = os.environ | {"SLURMROOT": self._slurm_root}
         result = subprocess.run(
-            [self._sbatch_bin, script], env=env, check=True, shell=False, capture_output=True, encoding="utf-8"
+            [str(self._sbatch_bin), str(script)],
+            env=env,
+            check=True,
+            shell=False,
+            capture_output=True,
+            encoding="utf-8",
         )
         # TODO the code initially had a TODO to write these two to a file, in general I think the logs of the squeue
         #      are currently not written to a file at all.
diff --git a/src/bfabric_scripts/bfabric_list_not_available_proteomics_workunits.py b/src/bfabric_scripts/bfabric_list_not_available_proteomics_workunits.py
index 94ed4452..063c59b9 100755
--- a/src/bfabric_scripts/bfabric_list_not_available_proteomics_workunits.py
+++ b/src/bfabric_scripts/bfabric_list_not_available_proteomics_workunits.py
@@ -13,77 +13,9 @@
 from __future__ import annotations
 
 from argparse import ArgumentParser
-from datetime import datetime, timedelta
 
-from loguru import logger
-from rich.console import Console
-from rich.table import Column, Table
-
-from bfabric import Bfabric
 from bfabric.cli_formatting import setup_script_logging
-from bfabric.entities import Parameter, Workunit, Application
-
-
-def render_output(workunits_by_status: dict[str, list[Workunit]], client: Bfabric) -> None:
-    """Renders the output as a table."""
-    table = Table(
-        Column("Application", no_wrap=False),
-        Column("WU ID", no_wrap=True),
-        Column("Created", no_wrap=True),
-        Column("Status", no_wrap=True),
-        Column("Created by", no_wrap=True, max_width=12),
-        Column("Name", no_wrap=False),
-        Column("Nodelist", no_wrap=False),
-    )
-
-    workunit_ids = [wu.id for wu_list in workunits_by_status.values() for wu in wu_list]
-    app_ids = {wu["application"]["id"] for wu_list in workunits_by_status.values() for wu in wu_list}
-
-    nodelist_params = Parameter.find_by({"workunitid": workunit_ids, "key": "nodelist"}, client)
-    nodelist_values = {param["workunit"]["id"]: param.value for param in nodelist_params.values()}
-    application_values = Application.find_all(ids=sorted(app_ids), client=client)
-
-    for status, workunits_all in workunits_by_status.items():
-        workunits = [x for x in workunits_all if x["createdby"] not in ["gfeeder", "itfeeder"]]
-        status_color = {
-            "Pending": "yellow",
-            "Processing": "blue",
-            "Failed": "red",
-        }.get(status, "black")
-
-        for wu in workunits:
-            app = application_values[wu["application"]["id"]]
-            table.add_row(
-                f"[link={app.web_url}]A{wu['application']['id']:3} {app['name']}[/link]",
-                f"[link={wu.web_url}&tab=details]WU{wu['id']}[/link]",
-                wu["created"],
-                f"[{status_color}]{status}[/{status_color}]",
-                wu["createdby"],
-                wu["name"],
-                nodelist_values.get(wu.id, "N/A"),
-            )
-
-    console = Console()
-    console.print(table)
-
-
-def list_not_available_proteomics_workunits(date_cutoff: datetime) -> None:
-    """Lists proteomics work units that are not available on bfabric."""
-    client = Bfabric.from_config()
-    console = Console()
-    with console.capture() as capture:
-        console.print(
-            f"listing not available proteomics work units created after {date_cutoff}", style="bright_yellow", end=""
-        )
-    logger.info(capture.get())
-
-    workunits_by_status = {}
-    for status in ["Pending", "Processing", "Failed"]:
-        workunits_by_status[status] = Workunit.find_by(
-            {"status": status, "createdafter": date_cutoff.isoformat()}, client=client
-        ).values()
-
-    render_output(workunits_by_status, client=client)
+from bfabric_scripts.cli.workunit.not_available import list_not_available_proteomics_workunits
 
 
 def main() -> None:
@@ -92,8 +24,7 @@ def main() -> None:
     parser = ArgumentParser(description="Lists proteomics work units that are not available on bfabric.")
     parser.add_argument("--max-age", type=int, help="Max age of work units in days", default=14)
     args = parser.parse_args()
-    date_cutoff = datetime.today() - timedelta(days=args.max_age)
-    list_not_available_proteomics_workunits(date_cutoff)
+    list_not_available_proteomics_workunits(max_age=args.max_age)
 
 
 if __name__ == "__main__":
diff --git a/src/bfabric_scripts/bfabric_save_workflowstep.py b/src/bfabric_scripts/bfabric_save_workflowstep.py
index f74e66ef..5ff8142c 100755
--- a/src/bfabric_scripts/bfabric_save_workflowstep.py
+++ b/src/bfabric_scripts/bfabric_save_workflowstep.py
@@ -42,8 +42,8 @@ def save_workflowstep(workunit_id: int | None = None) -> None:
     }
 
     workunit = client.read("workunit", obj={"id": workunit_id}).to_list_dict()[0]
-    application_id = workunit["application"]["_id"]
-    container_id = workunit["container"]["_id"]
+    application_id = workunit["application"]["id"]
+    container_id = workunit["container"]["id"]
 
     if application_id in workflowtemplatestep_ids and application_id in workflowtemplate_ids:
         workflows = client.read("workflow", obj={"containerid": container_id}).to_list_dict()
@@ -70,7 +70,7 @@ def save_workflowstep(workunit_id: int | None = None) -> None:
                 "workflowtemplatestepid": workflowtemplatestep_ids[application_id],
                 "workunitid": workunit_id,
             },
-        ).to_list_dict()
+        )
         print(res[0])
 
 
diff --git a/src/bfabric_scripts/bfabric_upload_submitter_executable.py b/src/bfabric_scripts/bfabric_upload_submitter_executable.py
index 052a4d77..46cfa333 100755
--- a/src/bfabric_scripts/bfabric_upload_submitter_executable.py
+++ b/src/bfabric_scripts/bfabric_upload_submitter_executable.py
@@ -35,65 +35,11 @@
 from __future__ import annotations
 
 import argparse
-import base64
 from pathlib import Path
 
-import yaml
-
 from bfabric import Bfabric
 from bfabric.cli_formatting import setup_script_logging
-
-
-def slurm_parameters() -> list[dict[str, str]]:
-    parameters = [{"modifiable": "true", "required": "true", "type": "STRING"} for _ in range(3)]
-    parameters[0]["description"] = "Which Slurm partition should be used."
-    parameters[0]["enumeration"] = ["prx"]
-    parameters[0]["key"] = "partition"
-    parameters[0]["label"] = "partition"
-    parameters[0]["value"] = "prx"
-    parameters[1]["description"] = "Which Slurm nodelist should be used."
-    parameters[1]["enumeration"] = ["fgcz-r-033"]
-    parameters[1]["key"] = "nodelist"
-    parameters[1]["label"] = "nodelist"
-    parameters[1]["value"] = "fgcz-r-[035,028]"
-    parameters[2]["description"] = "Which Slurm memory should be used."
-    parameters[2]["enumeration"] = ["10G", "50G", "128G", "256G", "512G", "960G"]
-    parameters[2]["key"] = "memory"
-    parameters[2]["label"] = "memory"
-    parameters[2]["value"] = "10G"
-    return parameters
-
-
-def main_upload_submitter_executable(
-    client: Bfabric, filename: Path, engine: str, name: str | None, description: str | None
-) -> None:
-    executable = filename.read_text()
-
-    attr = {
-        "context": "SUBMITTER",
-        "parameter": [],
-        "masterexecutableid": 11871,
-        "status": "available",
-        "enabled": "true",
-        "valid": "true",
-        "base64": base64.b64encode(executable.encode()).decode(),
-    }
-
-    if engine == "slurm":
-        name = name or "yaml / Slurm executable"
-        description = description or "Submitter executable for the bfabric functional test using Slurm."
-        attr["version"] = "1.03"
-        attr["parameter"] = slurm_parameters()
-    else:
-        raise NotImplementedError
-
-    if name:
-        attr["name"] = name
-    if description:
-        attr["description"] = description
-
-    res = client.save("executable", attr)
-    print(yaml.dump(res))
+from bfabric_scripts.cli.external_job.upload_submitter_executable import upload_submitter_executable_impl
 
 
 def main() -> None:
@@ -111,7 +57,7 @@ def main() -> None:
     parser.add_argument("--name", type=str, help="Name of the submitter", required=False)
     parser.add_argument("--description", type=str, help="Description about the submitter", required=False)
     options = parser.parse_args()
-    main_upload_submitter_executable(client=client, **vars(options))
+    upload_submitter_executable_impl(client=client, **vars(options))
 
 
 if __name__ == "__main__":
diff --git a/src/bfabric_scripts/cli/__init__.py b/src/bfabric_scripts/cli/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/bfabric_scripts/cli/__main__.py b/src/bfabric_scripts/cli/__main__.py
new file mode 100644
index 00000000..0fdf9bf9
--- /dev/null
+++ b/src/bfabric_scripts/cli/__main__.py
@@ -0,0 +1,13 @@
+import cyclopts
+
+from bfabric_scripts.cli.cli_external_job import app as _app_external_job
+from bfabric_scripts.cli.cli_read import app as _app_read
+from bfabric_scripts.cli.cli_workunit import app as _app_workunit
+
+app = cyclopts.App()
+app.command(_app_read, name="read")
+app.command(_app_external_job, name="external-job")
+app.command(_app_workunit, name="workunit")
+
+if __name__ == "__main__":
+    app()
diff --git a/src/bfabric_scripts/cli/cli_external_job.py b/src/bfabric_scripts/cli/cli_external_job.py
new file mode 100644
index 00000000..8afb1329
--- /dev/null
+++ b/src/bfabric_scripts/cli/cli_external_job.py
@@ -0,0 +1,61 @@
+import shutil
+from pathlib import Path
+from typing import Literal
+
+import cyclopts
+from rich.pretty import pprint
+
+from bfabric import Bfabric
+from bfabric.wrapper_creator.bfabric_submitter import BfabricSubmitter
+from bfabric.wrapper_creator.bfabric_wrapper_creator import BfabricWrapperCreator
+from bfabric_scripts.cli.external_job.upload_submitter_executable import upload_submitter_executable_impl
+from bfabric_scripts.cli.external_job.upload_wrapper_creator_executable import upload_wrapper_creator_executable_impl
+
+app = cyclopts.App()
+
+
+def find_slurm_root() -> str:
+    sbatch_path = shutil.which("sbatch")
+    if sbatch_path:
+        return str(Path(sbatch_path).parents[1])
+    else:
+        return "/usr/"
+
+
+@app.command
+def submitter(external_job_id: int, scheduler: Literal["Slurm"] = "Slurm") -> None:
+    if scheduler != "Slurm":
+        raise NotImplementedError(f"Unsupported scheduler: {scheduler}")
+    slurm_root = find_slurm_root()
+    client = Bfabric.from_config()
+    submitter = BfabricSubmitter(
+        client=client, externaljobid=external_job_id, scheduleroot=slurm_root, scheduler="Slurm"
+    )
+    submitter.submitter_yaml()
+
+
+@app.command
+def wrapper_creator(external_job_id: int) -> None:
+    client = Bfabric.from_config()
+    creator = BfabricWrapperCreator(client=client, external_job_id=external_job_id)
+    pprint(creator.create())
+
+
+@app.command
+def upload_submitter_executable(
+    filename: Path,
+    *,
+    engine: Literal["slurm"] = "slurm",
+    name: str = "yaml / Slurm executable",
+    description: str = "Submitter executable for the bfabric functional test using Slurm.",
+) -> None:
+    client = Bfabric.from_config()
+    upload_submitter_executable_impl(
+        client=client, filename=filename, engine=engine, name=name, description=description
+    )
+
+
+@app.command
+def upload_wrapper_creator_executable(filename: Path) -> None:
+    client = Bfabric.from_config()
+    upload_wrapper_creator_executable_impl(client=client, filename=filename)
diff --git a/src/bfabric_scripts/cli/cli_read.py b/src/bfabric_scripts/cli/cli_read.py
new file mode 100644
index 00000000..495fb946
--- /dev/null
+++ b/src/bfabric_scripts/cli/cli_read.py
@@ -0,0 +1,165 @@
+from __future__ import annotations
+
+import json
+import time
+from enum import Enum
+from typing import Any
+
+import cyclopts
+import yaml
+from loguru import logger
+from pydantic import BaseModel
+from rich.console import Console
+from rich.pretty import pprint
+from rich.table import Table
+
+from bfabric import Bfabric, BfabricClientConfig
+from bfabric.cli_formatting import setup_script_logging
+
+
+class OutputFormat(Enum):
+    JSON = "json"
+    YAML = "yaml"
+    TABLE_RICH = "table_rich"
+    AUTO = "auto"
+
+
+app = cyclopts.App()
+
+
+class CommandRead(BaseModel):
+    format: OutputFormat
+    limit: int
+    query: dict[str, str]
+    columns: list[str] | None
+    max_columns: int
+
+
+@app.default
+def bfabric_read(
+    endpoint: str,
+    attributes: list[tuple[str, str]] | None = None,
+    *,
+    output_format: OutputFormat = OutputFormat.AUTO,
+    limit: int = 100,
+    columns: list[str] | None = None,
+    max_columns: int = 7,
+) -> None:
+    """Reads one or several items from a B-Fabric endpoint and prints them.
+
+    Example usage:
+    read workunit name "DIANN%" createdafter 2024-10-31T19:00:00
+
+    :param endpoint: The endpoint to query.
+    :param attributes: A list of attribute-value pairs to filter the results by.
+    :param output_format: The output format to use.
+    :param limit: The maximum number of results to return.
+    :param columns: The columns to return (separate arguments).
+    :param max_columns: The maximum number of columns to return (only relevant if no columns are passed explicitly and a table output is chosen).
+    """
+    setup_script_logging()
+    client = Bfabric.from_config()
+    console_out = Console()
+
+    query = {attribute: value for attribute, value in attributes or []}
+    results = _get_results(client=client, endpoint=endpoint, query=query, limit=limit)
+    output_format = _determine_output_format(
+        console_out=console_out, output_format=output_format, n_results=len(results)
+    )
+    output_columns = _determine_output_columns(
+        results=results, columns=columns, max_columns=max_columns, output_format=output_format
+    )
+
+    if output_format == OutputFormat.JSON:
+        print(json.dumps(results, indent=2))
+    elif output_format == OutputFormat.YAML:
+        print(yaml.dump(results))
+    elif output_format == OutputFormat.TABLE_RICH:
+        pprint(
+            CommandRead(
+                format=output_format,
+                limit=limit,
+                query=query,
+                columns=output_columns,
+                max_columns=max_columns,
+            ),
+            console=console_out,
+        )
+        # _print_query_rich(console_out, query)
+        _print_table_rich(client.config, console_out, endpoint, results, output_columns=output_columns)
+    else:
+        raise ValueError(f"output format {output_format} not supported")
+
+
+def _determine_output_columns(
+    results: list[dict[str, Any]], columns: list[str] | None, max_columns: int, output_format: OutputFormat
+) -> list[str]:
+    if not columns:
+        if max_columns < 1:
+            raise ValueError("max_columns must be at least 1")
+        columns = ["id"]
+        available_columns = sorted(set(results[0].keys()) - {"id"})
+        columns += available_columns[:max_columns]
+
+    logger.info(f"columns = {columns}")
+    return columns
+
+
+def _get_results(client: Bfabric, endpoint: str, query: dict[str, str], limit: int) -> list[dict[str, Any]]:
+    start_time = time.time()
+    results = client.read(endpoint=endpoint, obj=query, max_results=limit)
+    end_time = time.time()
+    logger.info(f"number of query result items = {len(results)}")
+    logger.info(f"query time = {end_time - start_time:.2f} seconds")
+
+    results = sorted(results.to_list_dict(drop_empty=False), key=lambda x: x["id"])
+    if results:
+        possible_attributes = sorted(set(results[0].keys()))
+        logger.info(f"possible attributes = {possible_attributes}")
+
+    return results
+
+
+def _print_query_rich(
+    console_out: Console,
+    query: dict[str, str],
+) -> None:
+    pprint(query, console=console_out)
+
+
+def _print_table_rich(
+    config: BfabricClientConfig,
+    console_out: Console,
+    endpoint: str,
+    res: list[dict[str, Any]],
+    output_columns: list[str],
+) -> None:
+    """Prints the results as a rich table to the console."""
+    table = Table(*output_columns)
+    for x in res:
+        entry_url = f"{config.base_url}/{endpoint}/show.html?id={x['id']}"
+        values = []
+        for column in output_columns:
+            if column == "id":
+                values.append(f"[link={entry_url}]{x['id']}[/link]")
+            elif column == "groupingvar":
+                values.append(x.get(column, {}).get("name", "") or "")
+            elif isinstance(x.get(column), dict):
+                values.append(str(x.get(column, {}).get("id", "")))
+            else:
+                values.append(str(x.get(column, "")))
+        table.add_row(*values)
+    console_out.print(table)
+
+
+def _determine_output_format(console_out: Console, output_format: OutputFormat, n_results: int) -> OutputFormat:
+    """Returns the format to use, based on the number of results, and whether the output is an interactive console.
+    If the format is already set to a concrete value instead of "auto", it will be returned unchanged.
+    """
+    if output_format == OutputFormat.AUTO:
+        if n_results < 2:
+            output_format = OutputFormat.YAML
+        else:
+            output_format = OutputFormat.TABLE_RICH
+    logger.info(f"output format = {output_format}")
+    return output_format
diff --git a/src/bfabric_scripts/cli/cli_workunit.py b/src/bfabric_scripts/cli/cli_workunit.py
new file mode 100644
index 00000000..7f9f5ac1
--- /dev/null
+++ b/src/bfabric_scripts/cli/cli_workunit.py
@@ -0,0 +1,16 @@
+import cyclopts
+
+from bfabric.cli_formatting import setup_script_logging
+from bfabric_scripts.cli.workunit.not_available import list_not_available_proteomics_workunits
+
+app = cyclopts.App()
+
+
+@app.command
+def not_available(max_age: float = 14.0) -> None:
+    """Lists not available analysis work units.
+
+    :param max_age: The maximum age of work units in days.
+    """
+    setup_script_logging()
+    list_not_available_proteomics_workunits(max_age=max_age)
diff --git a/src/bfabric_scripts/cli/external_job/__init__.py b/src/bfabric_scripts/cli/external_job/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/bfabric_scripts/cli/external_job/upload_submitter_executable.py b/src/bfabric_scripts/cli/external_job/upload_submitter_executable.py
new file mode 100644
index 00000000..574f382c
--- /dev/null
+++ b/src/bfabric_scripts/cli/external_job/upload_submitter_executable.py
@@ -0,0 +1,58 @@
+from __future__ import annotations
+
+import base64
+from pathlib import Path
+
+import yaml
+
+from bfabric import Bfabric
+
+
+def slurm_parameters() -> list[dict[str, str]]:
+    parameters = [{"modifiable": "true", "required": "true", "type": "STRING"} for _ in range(3)]
+    parameters[0]["description"] = "Which Slurm partition should be used."
+    parameters[0]["enumeration"] = ["prx", "mascot"]
+    parameters[0]["key"] = "partition"
+    parameters[0]["label"] = "partition"
+    parameters[0]["value"] = "prx"
+    parameters[1]["description"] = "Which Slurm nodelist should be used."
+    parameters[1]["enumeration"] = ["fgcz-r-024", "fgcz-r-033", "fgcz-c-072", "fgcz-c-073"]
+    parameters[1]["key"] = "nodelist"
+    parameters[1]["label"] = "nodelist"
+    parameters[1]["value"] = "fgcz-r-[035,028]"
+    parameters[2]["description"] = "Which Slurm memory should be used."
+    parameters[2]["enumeration"] = ["10G", "50G", "128G", "256G", "512G", "960G"]
+    parameters[2]["key"] = "memory"
+    parameters[2]["label"] = "memory"
+    parameters[2]["value"] = "10G"
+    return parameters
+
+
+def upload_submitter_executable_impl(
+    client: Bfabric, filename: Path, engine: str, name: str | None, description: str | None
+) -> None:
+    executable = filename.read_text()
+
+    attr = {
+        "context": "SUBMITTER",
+        "parameter": [],
+        "masterexecutableid": 11871,
+        "status": "available",
+        "enabled": "true",
+        "valid": "true",
+        "base64": base64.b64encode(executable.encode()).decode(),
+    }
+
+    if engine == "slurm":
+        name = name or "yaml / Slurm executable"
+        description = description or "Submitter executable for the bfabric functional test using Slurm."
+        attr["version"] = "1.03"
+        attr["parameter"] = slurm_parameters()
+    else:
+        raise NotImplementedError
+
+    attr["name"] = name
+    attr["description"] = description
+
+    res = client.save("executable", attr)
+    print(yaml.dump(res))
diff --git a/src/bfabric_scripts/cli/external_job/upload_wrapper_creator_executable.py b/src/bfabric_scripts/cli/external_job/upload_wrapper_creator_executable.py
new file mode 100644
index 00000000..3d0176da
--- /dev/null
+++ b/src/bfabric_scripts/cli/external_job/upload_wrapper_creator_executable.py
@@ -0,0 +1,20 @@
+import base64
+from pathlib import Path
+
+from rich.pretty import pprint
+
+from bfabric import Bfabric
+
+
+def upload_wrapper_creator_executable_impl(client: Bfabric, filename: Path):
+    executable_content = filename.read_text()
+    attr = {
+        "name": "yaml 004",
+        "context": "WRAPPERCREATOR",
+        "parameter": None,
+        "description": "None.",
+        "masterexecutableid": 11851,
+        "base64": base64.b64encode(executable_content.encode()).decode(),
+    }
+    result = client.save("executable", attr)
+    pprint(result)
diff --git a/src/bfabric_scripts/cli/workunit/__init__.py b/src/bfabric_scripts/cli/workunit/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/bfabric_scripts/cli/workunit/not_available.py b/src/bfabric_scripts/cli/workunit/not_available.py
new file mode 100644
index 00000000..6fa4d8ef
--- /dev/null
+++ b/src/bfabric_scripts/cli/workunit/not_available.py
@@ -0,0 +1,73 @@
+from __future__ import annotations
+
+from datetime import datetime, timedelta
+
+from loguru import logger
+from rich.console import Console
+from rich.table import Column, Table
+
+from bfabric import Bfabric
+from bfabric.entities import Parameter, Workunit, Application
+
+
+def render_output(workunits_by_status: dict[str, list[Workunit]], client: Bfabric) -> None:
+    """Renders the output as a table."""
+    table = Table(
+        Column("Application", no_wrap=False),
+        Column("WU ID", no_wrap=True),
+        Column("Created", no_wrap=True),
+        Column("Status", no_wrap=True),
+        Column("Created by", no_wrap=True, max_width=12),
+        Column("Name", no_wrap=False),
+        Column("Nodelist", no_wrap=False),
+    )
+
+    workunit_ids = [wu.id for wu_list in workunits_by_status.values() for wu in wu_list]
+    app_ids = {wu["application"]["id"] for wu_list in workunits_by_status.values() for wu in wu_list}
+
+    nodelist_params = Parameter.find_by({"workunitid": workunit_ids, "key": "nodelist"}, client)
+    nodelist_values = {param["workunit"]["id"]: param.value for param in nodelist_params.values()}
+    application_values = Application.find_all(ids=sorted(app_ids), client=client)
+
+    for status, workunits_all in workunits_by_status.items():
+        workunits = [x for x in workunits_all if x["createdby"] not in ["gfeeder", "itfeeder"]]
+        status_color = {
+            "Pending": "yellow",
+            "Processing": "blue",
+            "Failed": "red",
+        }.get(status, "black")
+
+        for wu in workunits:
+            app = application_values[wu["application"]["id"]]
+            table.add_row(
+                f"[link={app.web_url}]A{wu['application']['id']:3} {app['name']}[/link]",
+                f"[link={wu.web_url}&tab=details]WU{wu['id']}[/link]",
+                wu["created"],
+                f"[{status_color}]{status}[/{status_color}]",
+                wu["createdby"],
+                wu["name"],
+                nodelist_values.get(wu.id, "N/A"),
+            )
+
+    console = Console()
+    console.print(table)
+
+
+def list_not_available_proteomics_workunits(max_age: float) -> None:
+    """Lists proteomics work units that are not available on bfabric."""
+    client = Bfabric.from_config()
+    date_cutoff = datetime.today() - timedelta(days=max_age)
+    console = Console()
+    with console.capture() as capture:
+        console.print(
+            f"listing not available proteomics work units created after {date_cutoff}", style="bright_yellow", end=""
+        )
+    logger.info(capture.get())
+
+    workunits_by_status = {}
+    for status in ["Pending", "Processing", "Failed"]:
+        workunits_by_status[status] = Workunit.find_by(
+            {"status": status, "createdafter": date_cutoff.isoformat()}, client=client
+        ).values()
+
+    render_output(workunits_by_status, client=client)
diff --git a/tests/bfabric/wrapper_creator/test_slurm.py b/tests/bfabric/wrapper_creator/test_slurm.py
index 3f375609..bc561982 100644
--- a/tests/bfabric/wrapper_creator/test_slurm.py
+++ b/tests/bfabric/wrapper_creator/test_slurm.py
@@ -23,7 +23,7 @@ def test_sbatch_when_success(mocker: MockerFixture, mock_slurm: SLURM, path: Pat
     assert stdout == "stdout"
     assert stderr == "stderr"
     mock_run.assert_called_once_with(
-        [Path("/tmp/test_slurm/bin/sbatch"), Path(path)],
+        ["/tmp/test_slurm/bin/sbatch", str(path)],
         env={"SLURMROOT": Path("/tmp/test_slurm"), "x": "y"},
         check=True,
         shell=False,