Fix WDL option spelling and tolerate Cromwell-isms (#4906)

* Fix WDL option spelling and tolerate Cromwell-isms * Linting. * Satisfy MyPy more (new MyPy?) --------- Co-authored-by: DailyDreaming <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
DataBiosphere · May 1, 2024 · 5d436d3 · 5d436d3
1 parent 2b4c044
commit 5d436d3
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 6 deletions.
diff --git a/docs/wdl/developing.rst b/docs/wdl/developing.rst
@@ -39,7 +39,7 @@ Cromwell::
 
 you can instead run with ``toil-wdl-runner``::
 
-    toil-wdl-runner myWorkflow.wdl --inputs myWorkflow_inputs.json
+    toil-wdl-runner myWorkflow.wdl --input myWorkflow_inputs.json
 
 .. _`official WDL tutorials`: https://wdl-docs.readthedocs.io/en/stable/
 .. _`executing your workflow`: https://wdl-docs.readthedocs.io/en/stable/WDL/execute/

diff --git a/docs/wdl/running.rst b/docs/wdl/running.rst
@@ -24,15 +24,18 @@ Instead of running a workflow with Cromwell::
 
 You can run the workflow with ``toil-wdl-runner``::
 
-    toil-wdl-runner myWorkflow.wdl --inputs myWorkflow_inputs.json
+    toil-wdl-runner myWorkflow.wdl --input myWorkflow_inputs.json
+
+(We're here running Toil with ``--input``, but it can also accept the
+Cromwell-style ``--inputs``.)
 
 This will default to executing on the current machine, with a job store in an
 automatically determined temporary location, but you can add a few Toil options
 to use other Toil-supported batch systems, such as Kubernetes::
 
-    toil-wdl-runner --jobStore aws:us-west-2:wdl-job-store --batchSystem kubernetes myWorkflow.wdl --inputs myWorkflow_inputs.json
+    toil-wdl-runner --jobStore aws:us-west-2:wdl-job-store --batchSystem kubernetes myWorkflow.wdl --input myWorkflow_inputs.json
 
-For Toil, the ``--inputs`` is optional, and inputs can be passed as a positional
+For Toil, the ``--input`` is optional, and inputs can be passed as a positional
 argument::
 
     toil-wdl-runner myWorkflow.wdl myWorkflow_inputs.json
@@ -58,7 +61,7 @@ directory.
 ``-m`` or ``--outputFile``: Specifies a JSON file name or URI to save workflow
 output values at. Defaults to standard output.
 
-``-i`` or ``--input``: Alternative to the positional argument for the
+``-i``, ``--input``, or ``--inputs``: Alternative to the positional argument for the
 input JSON file, for compatibility with other WDL runners.
 
 ``--outputDialect``: Specifies an output format dialect. Can be

diff --git a/src/toil/common.py b/src/toil/common.py
@@ -713,7 +713,7 @@ def check_arguments(typ: str) -> None:
                             help="WDL document URI")
         parser.add_argument("inputs_uri", type=str, nargs='?',
                             help="WDL input JSON URI")
-        parser.add_argument("--input", "-i", dest="inputs_uri", type=str,
+        parser.add_argument("--input", "--inputs", "-i", dest="inputs_uri", type=str,
                             help="WDL input JSON URI")
         check_arguments(typ="wdl")