📝 Update YAML sample for Pipeline Config

Author: shnizzedy

docs/_sources/user/pipelines/pipeline_config.rst

@@ -53,7 +53,7 @@ If you want to base a pipeline on another pipeline configuration YAML file, you
 
    FROM: /path/to/pipeline.yml
 
-in your pipeline configuration file. You can use the name of a :doc:`preconfigured pipeline </user/preconfig>` instead of a filepath if you want to base a configuration file on a preconfigured pipeline. If ``FROM`` is not specified, the pipeline will be based on :doc:`the default pipeline <default>`.
+in your pipeline configuration file. You can use the name of a :doc:`preconfigured pipeline </user/preconfig>` instead of a filepath if you want to base a configuration file on a preconfigured pipeline. If ``FROM`` is not specified, the pipeline will be based on :doc:`the default pipeline </user/pipelines/default>`.
 
 C-PAC will include all expected keys from the pipeline file specified in ``FROM`` (or the default pipeline if none is specified). Any keys specified in a pipeline configuration file will take precedence over the same key in the ``FROM`` base configuration, but all omitted keys will retain their values from the ``FROM`` base configuration.
 
@@ -67,28 +67,67 @@ If you want to run the analysis from terminal::
 
    cpac run --pipe_config {path to pipeline config} {path to data config}
 
-Pipeline configuration files, like the data settings and data configuration files discussed in the :doc:`data configuration builder section </user/subject_list_config>`, are stored as YAML files.  Similarly, each of the parameters used by C-PAC to assemble your pipeline can be specified as key-value pairs, so a pipeline configuration YAML would have multiple lines of the form ``key: value`` like so::
+Pipeline configuration files, like the data settings and data configuration files discussed in the :doc:`data configuration builder section </user/subject_list_config>`, are stored as YAML files.  Similarly, each of the parameters used by C-PAC to assemble your pipeline can be specified as nested key-value pairs, so a pipeline configuration YAML would have multiple lines of the form ``key: value`` like so
+
+.. code-block:: YAML
+
+    pipeline_setup:
 
     # Name for this pipeline configuration - useful for identification.
-    pipelineName :  pipeline01
+      pipelineName: pipeline01
+
+    working_directory:
+
+      # Directory where C-PAC should store temporary and intermediate files.
+      # - This directory must be saved if you wish to re-run your pipeline from where you left off (if not completed).
+      # - NOTE: As it stores all intermediate files, this directory can grow to become very
+      #   large, especially for data with a large amount of TRs.
+      # - If running in a container (Singularity/Docker), you can simply set this to an arbitrary
+      #   name like '/work', and then map (-B/-v) your desired output directory to that label.
+      # - If running outside a container, this should be a full path to a directory.
+      # - This can be written to '/tmp' if you do not intend to save your working directory.
+      path: /tmp
+
+      # Deletes the contents of the Working Directory after running.
+      # This saves disk space, but any additional preprocessing or analysis will have to be completely re-run.
+      remove_working_dir: True
+
+    crash_log_directory:
+
+      # Directory where CPAC should write crash logs.
+      path: /crash
+
+    log_directory:
+
+      # Whether to write log details of the pipeline run to the logging files.
+      run_logging: True
 
+      path: /logs
 
-    # Directory where CPAC should store temporary and intermediate files.
-    workingDirectory :  /home/runs/pipeline01/work
+    output_directory:
 
+      # Directory where C-PAC should write out processed data, logs, and crash reports.
+      # - If running in a container (Singularity/Docker), you can simply set this to an arbitrary
+      #   name like '/output', and then map (-B/-v) your desired output directory to that label.
+      # - If running outside a container, this should be a full path to a directory.
+      path: /output
 
-    # Directory where CPAC should write crash logs.
-    crashLogDirectory :  /home/runs/pipeline01/crash
+      # Include extra versions and intermediate steps of functional preprocessing in the output directory.
+      write_func_outputs: False
 
+      # Include extra outputs in the output directory that may be of interest when more information is needed.
+      write_debugging_outputs: False
 
-    # Directory where CPAC should place run logs.
-    logDirectory :  /home/runs/pipeline01/log
+      # Output directory format and structure.
+      # Options: default, ndmg
+      output_tree: "default"
 
+      # Generate quality control pages containing preprocessing and derivative outputs.
+      generate_quality_control_images: True
 
-    # Directory where CPAC should place processed data.
-    outputDirectory :  /home/runs/pipeline01/output
+An example of a pipeline configuration YAML file can be found :doc:`here </user/pipelines/default>`_.  Tables explaining the keys and their potential values can be found on the individual pages for each of the outputs C-PAC is capable of producing. All pipeline setup configuration files should have the keys in the :doc:`Output Settings </user/output_config>` table defined.
 
-An example of a pipeline configuration YAML file can be found `here <https://raw.githubusercontent.com/FCP-INDI/C-PAC/master/CPAC/resources/configs/pipeline_config_template.yml>`_.  Tables explaining the keys and their potential values can be found on the individual pages for each of the outputs C-PAC is capable of producing.  All pipeline configuration files should have the keys in the :doc:`Output Settings </user/output_config>` table defined.
+If ``FROM`` is defined (see above), any undefined keys will be inferred from the pipeline configuration specified; otherwise, any undefined keys will be inferred from the default pipeline.
 
 Why a list?
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