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[DOCS] Add examples of --list_sub_file/--list-sub-file #181

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Oct 18, 2024
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[DOCS] Add examples of --list_sub_file/--list-sub-file #181

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Update babs-init.rst to include examples of --list_sub_file
tientong98 Oct 18, 2024
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Update preparation_config_yaml_file.rst to include --list_sub_file ex…
tientong98 Oct 18, 2024
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Update preparation_config_yaml_file.rst
tientong98 Oct 18, 2024
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5 changes: 5 additions & 0 deletions docs/source/babs-init.rst
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Expand Up @@ -20,6 +20,11 @@ Command-Line Arguments
:ref:`how-to-define-name-of-input-dataset` below for general guidelines
and specific restrictions.

--list_sub_file, --list-sub-file : @after
Examples:
`Single-session example <https://github.com/PennLINC/babs/blob/ba32e8fd2d6473466d3c33a1b17dfffc4438d541/notebooks/initial_sub_list_single-ses.csv>`_,
`Multi-session example <https://github.com/PennLINC/babs/blob/ba32e8fd2d6473466d3c33a1b17dfffc4438d541/notebooks/initial_sub_list_multi-ses.csv>`_.

--keep_if_failed, --keep-if-failed : @after
These words below somehow refuse to appear in the built docs...
Please refer to below section
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1 change: 1 addition & 0 deletions docs/source/preparation_config_yaml_file.rst
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Expand Up @@ -147,6 +147,7 @@ Basics - Manual of writing section ``singularity_run``

* See below :ref:`advanced_manual_singularity_run` --> bullet point regarding
``--bids-filter-file`` for explanations.
* See :ref:`babs-init` for examples of ``--list_sub_file``/``--list-sub-file`` to filter subjects and sessions.

* :octicon:`alert-fill` :bdg-warning:`warning` Exception for positional arguments: if you have more than one input datasets,
you must use ``$INPUT_PATH`` to specify which dataset to use for the positional argument input BIDS dataset.
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