.. _installation:

Installation
************

Dependencies
============

This pipeline `Nextflow <https://www.nextflow.io/docs/latest/index.html>`_ requires `Docker <https://www.docker.com/>`_, `Singularity <https://sylabs.io/singularity/>`_ or `conda <https://conda.io/>`_ to run. Please read the information about how to proper :ref:`choose between conda, docker and singularity profiles<profiles>`.

1. Installing Nextflow

   .. code-block:: bash

      curl -s https://get.nextflow.io | bash

2. Download the pipeline

   .. code-block:: bash

      nextflow pull fmalmeida/ngs-preprocess

3. Test your installation

   .. code-block:: bash

      nextflow run fmalmeida/ngs-preprocess --help

4. Download required tools

   .. code-block:: bash
      
      # for docker
      docker pull fmalmeida/ngs-preprocess:v2.5
      nextflow run fmalmeida/ngs-preprocess -profile docker [options]

      # for singularity
      # remember to properly set NXF_SINGULARITY_LIBRARYDIR
      # read more at https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub
      export NXF_SINGULARITY_LIBRARYDIR=MY_SINGULARITY_IMAGES    # your singularity storage dir
      export NXF_SINGULARITY_CACHEDIR=MY_SINGULARITY_CACHE       # your singularity cache dir
      singularity pull \
            --dir $NXF_SINGULARITY_LIBRARYDIR \
            fmalmeida-ngs-preprocess-v2.5.img docker://fmalmeida/ngs-preprocess:v2.5
      nextflow run fmalmeida/ngs-preprocess -profile singularity [options]

      # for conda
      wget https://github.com/fmalmeida/ngs-preprocess/raw/master/environment.yml
      conda env create -f environment.yml # advice: use mamba
      nextflow run fmalmeida/ngs-preprocess -profile conda [options]

5. (Optional) Install nf-core

   ``pip install nf-core>=1.10``

.. note::

   Now, everything is set up and ready to run. Remember to always keep your Docker images up to date (Docker pull will always download the latest).