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RAP-840 Add Read the Docs

Merged RAP-840 Add Read the Docs
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Running the Pipeline
====================
The Pre-Processing Pipeline can be run from the command line using a CWL runner, e.g., ``cwltool`` or ``toil``:
Starting a pipeline run
-----------------------
The Pre-Processing Pipeline can be run from the command line using a CWL runner, e.g., ``cwltool`` or ``toil``. Below we describe how the pipeline can be run with these runners.
.. code:: console
$ cwltool $INSTALL_DIR/workflows/pipeline.cwl input.json
where ``$INSTALL_DIR`` refers to the location where the CWL files have been installed. Additionally, ``cwltool`` and ``toil``` come with a number of useful command line arguments, some of which are listed below. Please refer to their documentation for a full overview.
where ``$INSTALL_DIR`` refers to the location where the CWL files have been installed. Additionally, ``cwltool`` and ``toil`` come with a number of useful command line arguments, some of which are listed below. Please refer to their documentation for a full overview.
CWLTool options
---------------
.. note::
This section is a work in progress.
Toil options
------------
.. note::
This section is a work in progress.
Configuring the pipeline
------------------------
The parameters of the pipeline are provived as a JSON file. At the very least the pipeline requires a SASID be provided and input MeasurementSets (MSs), for instance:
.. code:: json
{
"sasid": "123456",
"msin": [
{
"class": "Directory",
"path": "/data/L888536_SAP000_SB026_uv.MS"
},
{
"class": "Directory",
"path": "/data/L888536_SAP000_SB027_uv.MS"
}
]
}
Refer to the :doc:`overview` section for a full overview of all pipeline parameters and features.
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