diff --git a/.github/workflows/verify_and_publish.yml b/.github/workflows/verify_and_publish.yml
index 8a281d55..1fd71427 100644
--- a/.github/workflows/verify_and_publish.yml
+++ b/.github/workflows/verify_and_publish.yml
@@ -159,7 +159,7 @@ jobs:
         coverage run \
           $(which cijoe) --monitor -l \
             --config cijoe-example-${{ matrix.usage_example }}/cijoe-config.toml \
-            --workflow cijoe-example-${{ matrix.usage_example }}/cijoe-workflow.yaml
+            cijoe-example-${{ matrix.usage_example }}/cijoe-workflow.yaml
 
     - name: Coverage report
       run: |
diff --git a/.gitignore b/.gitignore
index 95a6ec47..d4d1fb64 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
 .coverage
 cijoe-output*
+cijoe-archive*
 tags
 selftest_results
 *.egg-info
diff --git a/docs/source/050_usage_help.out b/docs/source/050_usage_help.out
index 9f6beeff..e2011a13 100644
--- a/docs/source/050_usage_help.out
+++ b/docs/source/050_usage_help.out
@@ -1,35 +1,36 @@
-usage: cijoe [-h] [--config CONFIG] [--workflow WORKFLOW] [--output OUTPUT]
-             [--log-level] [--monitor] [--no-report] [--skip-report]
-             [--tag TAG] [--archive] [--produce-report] [--integrity-check]
+usage: cijoe [-h] [--config CONFIG] [--output OUTPUT] [--log-level]
+             [--monitor] [--no-report] [--skip-report] [--tag TAG]
+             [--archive] [--produce-report] [--integrity-check]
              [--resources] [--example [EXAMPLE]] [--version]
-             [step ...]
+             [target] [step ...]
 
 options:
   -h, --help            show this help message and exit
 
-workflow:
-  Run workflow at '-w', using config at '-c', and output at '-o'
+run:
+  Options for running a workflow script.
 
-  step                  Given a workflow; one or more workflow steps to run.
-                        Else; one or more cijoe Python scripts to run.
-                        (default: None)
+  target                A cijoe workflow or script to run.
+  step                  Given a workflow, the steps of the workflow it
+                        should run. If none are given, all steps are
+                        run.
   --config CONFIG, -c CONFIG
-                        Path to the Configuration file. (default: cijoe-
-                        config.toml)
-  --workflow WORKFLOW, -w WORKFLOW
-                        Path to workflow file. (default: cijoe-workflow.yaml)
+                        Path a Configuration file. Multiple can be
+                        specified. (default: cijoe-config.toml)
+                        (default: [])
   --output OUTPUT, -o OUTPUT
-                        Path to output directory. (default: /cijoe/docs/cijoe-
-                        output)
-  --log-level, -l       Increase log-level. Provide '-l' for info and '-ll'
-                        for debug. (default: None)
+                        Path to output directory. (default:
+                        /cijoe/docs/cijoe-output)
+  --log-level, -l       Increase log-level. Provide '-l' for info and
+                        '-ll' for debug. (default: None)
   --monitor, -m         Dump command output to stdout (default: False)
-  --no-report, -n       Skip the producing, and opening, a report at the end
-                        of the workflow-run (default: False)
-  --skip-report, -s     Skip the report opening at the end of the workflow-run
-                        (default: True)
-  --tag TAG, -t TAG     Tags to identify a workflow-run. This will be prefixed
-                        while storing in archive (default: None)
+  --no-report, -n       Skip the producing, and opening, a report at the
+                        end of the workflow-run (default: False)
+  --skip-report, -s     Skip the report opening at the end of the
+                        workflow-run (default: True)
+  --tag TAG, -t TAG     Tags to identify a workflow-run. This will be
+                        prefixed while storing in archive (default:
+                        None)
 
 utilities:
   Workflow, and workflow-related utilities
@@ -39,13 +40,13 @@ utilities:
   --produce-report, -p  Produce report, and open it, for output at '-o /
                         --output' and exit. (default: None)
   --integrity-check, -i
-                        Check integrity of workflow at '-w / --workflow' and
-                        exit. (default: False)
-  --resources, -r       List collected resources and exit. (default: False)
+                        Check integrity of workflow given as positional
+                        argument and exit. (default: False)
+  --resources, -r       List collected resources and exit. (default:
+                        False)
   --example [EXAMPLE], -e [EXAMPLE]
-                        Emits the given example. When no example is given,
-                        then it prints a list of available examples. (default:
-                        None)
+                        Emits the given example. When no example is
+                        given, then it prints a list of available
+                        examples. (default: None)
   --version, -v         Print the version number of 'cijoe' and exit.
-                        (default: False)
-
+                        (default: False)
\ No newline at end of file
diff --git a/docs/source/usage/index.rst b/docs/source/usage/index.rst
index 6c61d500..4fad8d95 100644
--- a/docs/source/usage/index.rst
+++ b/docs/source/usage/index.rst
@@ -61,10 +61,10 @@ Which yields the following output:
 Search Paths
 ============
 
-The :ref:`sec-usage-cli` for the positional argument, and config-files 
-(``--c / --config``) and workflows (``-w / --workflow``) by default search for files
-named ``cijoe-workflow.yaml`` and ``cijoe-config.toml``, respectfully. These files
-are searched for, in order, in the following locations:
+The :ref:`sec-usage-cli` for the positional target argument, and for config-files 
+(``--c / --config``) by default search for files named ``cijoe-workflow.yaml``
+and ``cijoe-config.toml``, respectfully. These files are searched for, in order, 
+in the following locations:
 
 ``$PWD``
    In your current working directory
@@ -179,7 +179,7 @@ as an artifact.
          run: |
            $(which cijoe) --monitor -l \
              --config ./example/cijoe-config.toml \
-             --workflow ./example/cijoe-workflow.yaml
+            ./example/cijoe-workflow.yaml
 
        - name: Upload report
          if: always()
diff --git a/src/cijoe/cli/cli.py b/src/cijoe/cli/cli.py
index 1ec32e8d..a3c15ab6 100644
--- a/src/cijoe/cli/cli.py
+++ b/src/cijoe/cli/cli.py
@@ -459,45 +459,29 @@ def create_adhoc_workflow(args):
 def parse_args():
     """Parse command-line interface."""
 
-    parent_dirs = set()
-    is_workflow = False
-
-    for i, argv in enumerate(sys.argv):
-        if i == 0 or sys.argv[i - 1].startswith("-"):
-            continue
-        if argv.endswith(".py"):
-            path = Path(argv).resolve()
-            parent_dirs.add(path.parent)
-            sys.argv[i] = path.stem
-            break
-        if argv.endswith(".yaml"):
-            is_workflow = True
-            sys.argv.insert(i, "--workflow")
-            sys.argv.insert(i, "workflow_path")
-            break
-
-    resource_scripts = get_resources(list(parent_dirs))["scripts"]
-
+    # A parent parser is added without help text to allow for parsing part of the
+    # arguments and evaluating them before proceeding with parsing the rest
     parent_parser = argparse.ArgumentParser(add_help=False)
 
     run_group = parent_parser.add_argument_group(
         "run", "Options for running a workflow script."
     )
-
+    run_group.add_argument(
+        "target",
+        nargs="?",
+        default=None,
+        help="A cijoe workflow or script to run.",
+    )
     run_group.add_argument(
         "step",
         nargs="*",
         default=[],
         help="Given a workflow, the steps of the workflow it should run. If none are given, all steps are run.",
     )
-
     run_group.add_argument(
         "--workflow",
         "-w",
-        type=Path,
-        default=Path(
-            os.environ.get("CIJOE_DEFAULT_WORKFLOW", DEFAULT_WORKFLOW_FILENAME)
-        ),
+        default=None,
         help=argparse.SUPPRESS,
     )
     run_group.add_argument(
@@ -597,61 +581,79 @@ def parse_args():
         help="Print the version number of 'cijoe' and exit.",
     )
 
+    args, _ = parent_parser.parse_known_args()
+
+    # A parser inheriting from the parent_parser is added to allow for printing
+    # the help text if --help argument is given.
     parser = argparse.ArgumentParser(
         prog=Path(sys.argv[0]).stem,
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         parents=[parent_parser],
     )
 
-    subparsers = parser.add_subparsers()
-
-    # Create subparser for workflows
-    subparsers.add_parser(
-        "workflow_path", parents=[parent_parser], help="Path to a cijoe workflow file."
-    )
-    subparsers.add_parser("script_path", help="Path to a cijoe script.")
-    subparsers.add_parser(
-        "script_name",
-        help="Name of a cijoe script. You can see all reachable cijoe scripts with command 'cijoe -r'.",
-    )
-
-    # Create subparser for scripts
-    # Adding the subparser requires loading the whole script, so
-    # we only add the subparser to the script given in the arguments
-    if not is_workflow:
-        for i, argv in enumerate(sys.argv):
-            if i == 0 or argv.startswith("-") or sys.argv[i - 1].startswith("-"):
-                continue
-
-            # The first positional argument is the script identifier
-            ident = argv
-
-            script = resource_scripts.get(ident, None)
-            if not script:
-                log.error(f"Invalid target({ident})")
-                return errno.EINVAL, None
-            script.load()
-            help_text = (
-                next(line for line in script.docs.splitlines() if line)
-                if script.docs
-                else ""
-            )
-            subparser = subparsers.add_parser(
-                ident,
-                parents=[parent_parser],
-                help=help_text,
-                epilog=script.docs,
-                formatter_class=argparse.RawTextHelpFormatter,
-            )
-            subparser.add_argument(
-                "--script-name", default=ident, help=argparse.SUPPRESS
-            )
-            if script.argparser_func:
-                script.argparser_func(subparser)
-
-            break
-
-    args = parser.parse_args()
+    # For backwards compatibility: allow the --workflow argument.
+    # If the --workflow argument is used, and a positional argument is given, the
+    # parser will interpret it as a `target`, but we assume it to be a step
+    # identifier.
+    if args.workflow:
+        log.warning(
+            "The -w / --workflow argument is deprecated"
+            "please specify the workflow as a positional argument instead."
+        )
+        args = parser.parse_intermixed_args()
+        if args.target:
+            args.step = [args.target] + args.step
+        args.workflow = Path(args.workflow)
+
+    # If the target ends with .yaml, we run the workflow at the given path, and
+    # assume that the remaining positional args are step identifiers of the
+    # given workflow.
+    # note: the `parse_intermixed_args` allow for multiple groups of positional
+    # arguments, i.e. both the workflow path and step identifiers.
+    elif not args.target or args.target.endswith(".yaml"):
+        args = parser.parse_intermixed_args()
+        workflow = args.target or os.environ.get(
+            "CIJOE_DEFAULT_WORKFLOW", DEFAULT_WORKFLOW_FILENAME
+        )
+        setattr(args, "workflow", Path(workflow))
+
+    # Else, we assume the target is either a cijoe script identifier or path
+    else:
+        ident = args.target
+        parent_dirs = []
+
+        # If direct path to script is given, the parent directories must be
+        # included in the resource-collection
+        if ident.endswith(".py"):
+            path = Path(ident)
+            parent_dirs.append(path.parent)
+            ident = path.stem
+
+        resource_scripts = get_resources(parent_dirs)["scripts"]
+
+        # Load the script to get the name and arguments for the script, so
+        # arguments can be parsed and/or added to the help text
+        script = resource_scripts.get(ident, None)
+        if not script:
+            log.error(f"Invalid target({ident})")
+            return errno.EINVAL, None
+        script.load()
+
+        help_text = (
+            next(line for line in script.docs.splitlines() if line)
+            if script.docs
+            else ""
+        )
+        script_group = parser.add_argument_group(
+            help_text, "Options specific for the given script"
+        )
+        if script.argparser_func:
+            script.argparser_func(script_group)
+
+        args = parser.parse_args()
+
+        setattr(args, "script_name", ident)
+        args.step = []
 
     levels = [log.ERROR, log.INFO, log.DEBUG]
     log.basicConfig(
diff --git a/tests/core/test_argparse.py b/tests/core/test_argparse.py
new file mode 100644
index 00000000..e360f31b
--- /dev/null
+++ b/tests/core/test_argparse.py
@@ -0,0 +1,215 @@
+import copy
+import os
+import sys
+from argparse import Namespace
+from pathlib import Path
+
+from cijoe.cli.cli import DEFAULT_CONFIG_FILENAME, DEFAULT_WORKFLOW_FILENAME, parse_args
+
+TEMPLATE_SCRIPT = """def main(args, cijoe):
+    return 0
+"""
+
+
+def test_run_group():
+    """
+    Base test to check all arguments are set
+    """
+
+    config = "config.toml"
+    output = "output"
+    tag = "tag"
+    loglevel = "ll"
+    example = "example"
+
+    test_args = [
+        "cijoe",
+        "-c",
+        config,
+        "-o",
+        output,
+        f"-{loglevel}",
+        "--monitor",
+        "--no-report",
+        "--skip-report",
+        "--tag",
+        tag,
+        "--archive",
+        "--produce-report",
+        "--integrity-check",
+        "--resources",
+        "--example",
+        example,
+        "--version",
+    ]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.config[0].name == config
+    assert args.output.name == output
+    assert len(args.log_level) == len(loglevel)
+    assert args.monitor
+    assert args.no_report
+    assert not args.skip_report
+    assert args.tag == [tag]
+    assert args.archive
+    assert args.produce_report
+    assert args.integrity_check
+    assert args.resources
+    assert args.example == example
+    assert args.version
+
+
+def test_target_workflow():
+    workflow = "workflow.yaml"
+
+    test_args = ["cijoe", workflow]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.workflow.name == workflow
+
+
+def test_target_workflow_steps():
+    workflow = "workflow.yaml"
+    steps = ["step1", "step2", "step3"]
+
+    test_args = ["cijoe", workflow, *steps]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.workflow.name == workflow
+    assert len(args.step) == len(steps)
+    assert all(a == b for a, b in zip(args.step, steps))
+
+
+def test_target_core_script():
+    script = "core.example_script_default"
+
+    test_args = ["cijoe", script]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.script_name == script
+
+
+def test_target_core_script_args():
+    script = "core.example_script_default"
+
+    test_args = ["cijoe", script, "--repeat", "10"]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.script_name == script
+    assert args.repeat == 10
+
+
+def test_target_path_script(tmp_path):
+    script = "test"
+    script_path = (tmp_path / f"{script}.py").resolve()
+
+    script_path.write_text(TEMPLATE_SCRIPT)
+
+    test_args = ["cijoe", str(script_path)]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.script_name == script
+
+
+def test_target_path_script_args_fail(tmp_path):
+    """
+    If given a wrong argument, the argument parser should fail
+    """
+
+    script = "test"
+    script_path = (tmp_path / f"{script}.py").resolve()
+
+    script_path.write_text(TEMPLATE_SCRIPT)
+
+    test_args = ["cijoe", str(script_path), "--repeat", "10"]
+    sys.argv = test_args
+
+    try:
+        _ = parse_args()
+        assert False
+    except SystemExit:
+        assert True
+
+
+def test_target_path_script_step(tmp_path):
+    """
+    If given additional steps when running a script, the argument parser remove
+    the steps
+    """
+
+    steps = ["step1", "step2", "step3"]
+
+    script = "test"
+    script_path = (tmp_path / f"{script}.py").resolve()
+
+    script_path.write_text(TEMPLATE_SCRIPT)
+
+    test_args = ["cijoe", str(script_path), *steps]
+    sys.argv = test_args
+
+    err, args = parse_args()
+    assert not err
+    assert args.script_name == script
+    assert not args.step
+
+
+def test_workflow_argument():
+    """
+    For backwards compatibility, the -w / --workflow argument should still work
+    """
+
+    workflow = "workflow.yaml"
+
+    test_args = ["cijoe", "-w", workflow]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.workflow.name == workflow
+
+
+def test_workflow_argument_steps():
+    """
+    For backwards compatibility, the -w / --workflow argument should still work
+    """
+
+    workflow = "workflow.yaml"
+    steps = ["step1", "step2", "step3"]
+
+    test_args = ["cijoe", "-w", workflow, *steps]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.workflow.name == workflow
+    assert len(args.step) == len(steps)
+    assert all(a == b for a, b in zip(args.step, steps))
+
+
+def test_mixed_order():
+    config = "config.toml"
+    workflow = "workflow.yaml"
+    steps = ["step1", "step2", "step3"]
+
+    test_args = ["cijoe", "-c", config, "--monitor", workflow, *steps, "-l"]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.workflow.name == workflow
+    assert args.config[0].name == config
+    assert len(args.step) == len(steps)
+    assert all(a == b for a, b in zip(args.step, steps))
+
+
+def test_defaults():
+    test_args = ["cijoe"]
+    sys.argv = test_args
+    err, args = parse_args()
+    assert not err
+    assert args.workflow.name == os.environ.get(
+        "CIJOE_DEFAULT_WORKFLOW", DEFAULT_WORKFLOW_FILENAME
+    )