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RAP-840 Add Read the Docs

Merged Mick Veldhuis requested to merge rap-840-add-docs into main
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@@ -30,14 +30,16 @@ Since the Pre-Processing Pipeline is running inside a container, do not forgot t
There are a number of command-line options you might want consider adding when running ``cwltool``:
* ``--outdir``: specifies the (relative) path to the directory containing the output of the pipeline
* ``--log-dir``: specifies the location of the log files produces by the ``stdout`` and ``stderr`` of a ``CommandLineTool``
* ``--outdir``: specifies the (relative) path to the directory containing the output of the pipeline (make sure to mount this directory when running the pipeline in a container)
* ``--log-dir``: specifies the location of the log files produces by the ``stdout`` and ``stderr`` of a ``CommandLineTool`` (make sure to mount this directory when running the pipeline in a container)
* ``--preserve-entire-environment``: use your system's environment variables when manually installing the dependencies
* ``--no-container``: do not execute jobs in a container (add this when the dependencies have been installed manually)
* ``--singularity``: use the Apptainer (previously Singularity) runtime for running containers instead of Docker
* ``--debug``: more verbose output, useful when debugging
Running the pipeline without the ``--no-container`` option will always attempt to run the steps inside their respective (Docker) container. A full overview of CLI arguments is available in their `documentation <https://cwltool.readthedocs.io/en/latest/cli.html>`_.
Running the pipeline without the ``--no-container`` option will always attempt to run the steps inside their respective (Docker) container. Make sure to mount the output and log directories, specified by ``--outdir`` and ``--log-dir``, when running the pipeline inside a container to ensure the files are not lost after execution.
A full overview of CLI arguments is available in their `documentation <https://cwltool.readthedocs.io/en/latest/cli.html>`_.
``toil`` options
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@@ -55,6 +57,8 @@ Similarly, these options might be of interest when using ``toil``:
* ``--singularity``: use the Apptainer (previously Singularity) runtime for running containers instead of Docker
* ``--stats``: with this option Toil collects runtime statistics (they can be used by ``toil stats``)
Make sure to mount the output, log directories, and working directories, when running the pipeline inside a container to ensure the files are not lost after execution.
A full overview of CLI arguments is available in their `documentation <https://toil.readthedocs.io/en/latest/running/cliOptions.html>`_.
Configuring the pipeline
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