.. _run:

Running
=======

The pipeline offers a workflow that processes files, images, and 
builds a Vitessce config file from the generated files.
Alternatively, the workflow to process files only, or the workflow to process images only  
can be called independently.

Each of these workflows work as entry points that can be specified when running the
pipeline through the command line.

- The ``Full_pipeline`` workflow runs the other workflows as needed and
  builds a Vitessce config file per dataset.
- The ``Process_files`` workflow handles data files and their conversions.
- The ``Process_images`` workflow handles image files and/or label image data and their conversions.

The pipeline configuration and the location of input data is specified through the 
:ref:`parameters yaml file <parameters_file>`. This file is passed to Nextflow when
running the pipeline. 

To run the ``Full_pipeline`` use

.. code-block:: shell

   nextflow run main.nf -params-file /path/to/params.yaml -entry Full_pipeline


This will handle all input files, whether they are data files or images, for all datasets
defined.

You can modify the entry point if you're interested in only getting the converted outputs.
Use ``-entry Process_files`` or ``-entry Process_images`` as you need.

Running using Conda 
-------------------

The default pipeline will run on local executor without any type of environment creation. To run the pipeline using conda environments use the ``-profile conda`` option:

.. code-block:: shell

   nextflow run main.nf \
            -params-file /path/to/params.yaml \
            -entry Full_pipeline \
            -profile conda

Creating the environment when the pipeline is launched may take a few minutes.

Running using Docker 
--------------------

The default pipeline will run on local executor without any type of environment creation. To run the pipeline using Docker containers use the ``-profile docker`` option:

.. code-block:: shell

   nextflow run main.nf \
            -params-file /path/to/params.yaml \
            -entry Full_pipeline \
            -profile docker

Pulling the containers when the pipline is launched may take a few minutes.

Running using Singularity 
-------------------------

The default pipeline will run on local executor without any type of environment creation. To run the pipeline using Singularity containers use the ``-profile singularity`` option:

.. code-block:: shell

   nextflow run main.nf \
            -params-file /path/to/params.yaml \
            -entry Full_pipeline \
            -profile singularity

Pulling the containers when the pipline is launched may take a few minutes.

Further reading
---------------

For more information about Docker image pulling/local conda env creation in Nextflow please refer to Nextflow's official docs for `containers <https://www.nextflow.io/docs/latest/container.html>`__ and `conda <https://www.nextflow.io/docs/latest/conda.html>`__.