This MR adds Read the Docs documentation pages. It includes:
Installation instructions
Instructions to run the pipeline
A basic overview of the operations and adjustable parameters
Given that the pipeline is still very much in development, a lot of this information is subject to change. This is just a first pass at the user documentation.
Instructions for downloading and installing the Pre-Processing Pipeline are summarised below and also available on the GitLab page.
Instructions for downloading and installing the Pre-Processing Pipeline are summarised below and also available on its `GitLab page <https://git.astron.nl/RD/preprocessing-cwl>`_.
Obtaining the Pre-Processing Pipeline
-------------------------------------
Perform a git clone.
The pipeline consists of Common Workflow Language (CWL) workflows, which can be obtained with:
To run the pipeline, you need a CWL runner, such as ``cwltool`` or ``toil``. It's recommended to install these in a virtual environment:
.. code:: console
$ python3 -m venv venv
$ source venv/bin/active
$ pip install cwltool toil[cwl]
Note that it is also necessary to install NodeJS, which can either be installed via your favourite package manager or using the ``nodejs-wheel`` Python package.
Additionally, the Pre-Processing Pipeline depends on the following software for processing: