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Changes to organization of 'Setting Up A Pipeline' page
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‎docs/user/_images/deriv_gui.png‎

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‎docs/user/_images/output_gui.png‎

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‎docs/user/_images/preprocwf_gui.png‎

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‎docs/user/_sources/deriv_config.txt‎

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Derivatives Settings
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---------------------
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.. figure:: /_images/deriv_gui.png
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Configuration Without the GUI
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""""""""""""""""""""""""""""""
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The following key/value pairs must be defined in your :doc:`pipeline configuration YAML </pipeline_config>` for C-PAC to run:
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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| Key | Description | Potential Values |
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+===============================+==============================================================================================================================+====================================================================================+
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| runZScoring | Determines format of outputs. 0 will produce non-z-scored outputs, 1 will produce z-scores of outputs. | A list where '1' represents 'yes' and '0' represents 'no' (e.g., '[1]'). |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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The box below contains an example of what these parameters might look like when defined in the YAML::
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runZScoring : [1]

‎docs/user/_sources/output_config.txt‎

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Output Settings
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----------------
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.. figure:: /_images/output_gui.png
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Configuration Without the GUI
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""""""""""""""""""""""""""""""
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The following key/value pairs must be defined in your :doc:`pipeline configuration YAML </pipeline_config>` for C-PAC to run:
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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| Key | Description | Potential Values |
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+===============================+==============================================================================================================================+====================================================================================+
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| pipelineName | A name that you would like to give to this pipeline. | A string. |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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| workingDirectory | The working directory to be used by the pipeline during the run. | A path (e.g.,'/data/my_analysis/working'). |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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| crashLogDirectory | The directory where C-PAC will store crash logs. | A path (e.g.,'/data/my_analysis/crash'). |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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| outputDirectory | The output directory for the pipeline. | A path (e.g.,'/data/my_analysis/output'). |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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| runSymbolicLinks | Create a user-friendly, well-organized version of the output directory. | A list where '1' represents 'yes' and '0' represents 'no' (e.g., '[1]'). |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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| generateQualityControlImages | Generate quality control pages containing preprocessing and derivative outputs. | A list where '1' represents 'yes' and '0' represents 'no' (e.g., '[1]'). |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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| removeWorkingDir | Deletes the contents of the Working Directory after running. Saves disk space, but steps will need to be re-run. | True,False |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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| reGenerateOutputs | Uses the contents of the Working Directory to regenerate all outputs and their symbolic links. | True,False |
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+-------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------+
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The box below contains an example of what these parameters might look like when defined in the YAML::
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pipelineName : gelastic_epilepsy_pipeline
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workingDirectory : /data/working
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crashLogDirectory : /data/crash
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outputDirectory : /data/output
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runSymbolicLinks : [1]
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generateQualityControlImages : [1]
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removeWorkingDir : False
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reGenerateOutputs : False

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