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updated documentation to include information about paths
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Leahh02 committed Sep 20, 2024
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5 changes: 3 additions & 2 deletions docs/sphinx/commands.rst
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Expand Up @@ -103,9 +103,10 @@ Arguments:
``beeflow reexecute``: Reexecute an archived workflow.

Arguments:
WF_ID [required]
- WF_ID [required]
- OUTPUT_DIR, Path to the where the DAG directory will be [required]

``beeflow dag``: Export a directed acyclic graph (DAG) of a submitted workflow. This command can be run at any point of the workflow. To see the DAG of a workflow before it runs, submit the workflow with the ``--no-start`` flag and then use the dag command. The DAGs are exported to ~/.beeflow/dags. See :ref:`workflow-visualization` for more information.
``beeflow dag``: Export a directed acyclic graph (DAG) of a submitted workflow. This command can be run at any point of the workflow. To see the DAG of a workflow before it runs, submit the workflow with the ``--no-start`` flag and then use the dag command. The DAGs are exported to $OUTPUT_DIR/$WD_ID_dags. See :ref:`workflow-visualization` for more information.

Arguments:
WF_ID [required]
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5 changes: 2 additions & 3 deletions docs/sphinx/visualization.rst
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Expand Up @@ -4,7 +4,7 @@ Workflow Visualization
**********************

BEE includes a simple command for viewing BEE workflows. By using the ``beeflow
dag $ID`` command, you can view the directed acyclic graph (DAG) of any submitted
dag $ID $OUTPUT_DIR`` command, you can view the directed acyclic graph (DAG) of any submitted
workflow.

Creating DAGs
Expand All @@ -13,8 +13,7 @@ Creating DAGs
The dag command can be run at any point of the workflow, and can
be run multiple times. To see the DAG of a workflow before it runs, submit
the workflow with the ``--no-start`` flag and then use the dag command. The
DAGs are exported in PNG format to ~/.beeflow/dags. They follow the naming
convention ``$ID.png``
DAGs are exported in PNG format to $OUTPUT_DIR/$WD_ID_dags.

Example DAG
===========
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