Merge pull request #183 from PennLINC/docs/add_eg_list_sub_file

[DOCS] Add examples of --list_sub_file/--list-sub-file - Fixed rendering issues

docs/source/babs-init.rst

@@ -20,11 +20,6 @@ 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
@@ -86,7 +81,9 @@ How is the list of subjects (and sessions) determined?
 A list of subjects (and sessions) will be determined when running ``babs-init``,
 and will be saved in a CSV file called named ``sub_final_inclu.csv`` (for single-session dataset)
 or ``sub_ses_final_inclu.csv`` (for multiple-session dataset),
-located at ``/path/to/my_BABS_project/analysis/code``
+located at ``/path/to/my_BABS_project/analysis/code``.
+
+**To filter subjects and sessions**, use ``babs-init`` with ``--list-sub-file /path/to/subject/list/csv/file``. 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>`_.
 
 See :ref:`list_included_subjects` for how this list is determined.
 

docs/source/preparation_config_yaml_file.rst

@@ -147,7 +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.
+            * See :doc:`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.