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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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@@ -23,6 +23,7 @@ There are a number of command-line options you might want consider adding when r
* ``--log-dir``: specifies the location of the log files produces by the ``stdout`` and ``stderr`` of a ``CommandLineTool``
* ``--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>`_.
@@ -40,6 +41,7 @@ Similarly, these options might be of interest when using ``toil``:
* ``—batchSystem``: use a specific batch system of a HPC cluster (e.g., ``slurm`` or ``single_machine``)
* ``--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
* ``--stats``: with this option Toil collects runtime statistics (they can be used by ``toil stats``)
A full overview of CLI arguments is available in their `documentation <https://toil.readthedocs.io/en/latest/running/cliOptions.html>`_.
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