.. _`ris-nextflow-quickstart`:

========
Nextflow
========

.. contents::
   :depth: 1
   :local:

.. admonition:: Compute Resources

    - Have questions or need help with compute, including activation or issues?
      Follow `this link. <https://washu.atlassian.net/servicedesk/customer/portal/2/group/6/create/43>`__
    - :ref:`User Agreement <compute-user-agreement>`

.. admonition:: Docker Usage

    - The information on this page assumes that you have a knowledge base of
      using Docker to create images and push them to a repository for use. If
      you need to review that information, please see the links below.
    - :ref:`Docker and the RIS Compute Service <docker-on-compute>`
    - :ref:`Docker Basics: Building, Tagging, & Pushing A Custom Docker Image <ris-docker-basics>`

.. _`ris-nextflow-quickstart-gui`:

Interactive GUI Session
-----------------------

- Interactive GUI sessions are done via Open On Demand (OOD).
    - You can use the ``Compute RIS Desktop`` application.
- You can find out more about OOD here: :ref:`Compute Quick Start <compute-quick-start>`.
- Fill out the fields with the appropriate information (explained in the quick start).
- Launch the ``Compute RIS Desktop`` application, and follow the steps below.
    - Include the following in the ``Mounts`` field.

    .. code::

        /scratch1/fs1/ris:/scratch1/fs1/ris

    - Once in an interactive session the following is an example command of using Nextflow.

    .. code::

        nextflow run nf-core/rnaseq \
        -profile test \
        -c /scratch1/fs1/ris/application/nextflow/conf/rnaseq.config \
        --outdir /path/to/outdir


.. _`ris-nextflow-quickstart-cli`:

Command-Line Sessions
---------------------

.. Note::

    If you are a member of more than one compute group, you will be prompted to specify an LSF User Group with ``-G group_name`` or by setting the ``LSB_SUB_USER_GROUP`` variable.

Interactive Session
~~~~~~~~~~~~~~~~~~~

- If users wish to use Nextflow in an interactive command-line session, it can be done via the THPC terminal.
- Users can find out about using the THPC terminal :ref:`here.<ris-thpc-quickstart-cli>`
- Users can use Nextflow just like with OOD.
- Users must include ``/scratch1/fs1/ris:/scratch1/fs1/ris`` in the ``LSF_DOCKER_VOLUMES`` environment variable.
- Make sure the directory to be used as the Nextflow working directory is included in the ``LSF_DOCKER_VOLUMES`` environment variable.

.. code::

    LSF_DOCKER_VOLUMES="/scratch1/fs1/ris:/scratch1/fs1/ris /storage1/fs1/${STORAGE_ALLOCATION}/Active:/storage1/fs1/{$STORAGE_ALLOCATION}/Active" \
    thpc-terminal bash -c "cd /path/to/nextflow/working/directory ; nextflow run nf-core/sarek -profile test -c /scratch1/fs1/ris/application/nextflow/conf/rnaseq.config --outdir /path/to/nextflow/working/directory"

- ``/path/to/nextflow/working/directory`` is the path to the Nextflow working directory.

Batch Session
~~~~~~~~~~~~~

- If users wish to use Nextflow in an batch session, it can be done via the THPC batch.
- Users can find out about using the THPC terminal :ref:`here.<ris-thpc-quickstart-cli>`
- Users must include ``/scratch1/fs1/ris:/scratch1/fs1/ris`` in the ``LSF_DOCKER_VOLUMES`` environment variable.
- Make sure the directory to be used as the Nextflow working directory is included in the ``LSF_DOCKER_VOLUMES`` environment variable.

.. code::

    LSF_DOCKER_VOLUMES="/scratch1/fs1/ris:/scratch1/fs1/ris /storage1/fs1/${STORAGE_ALLOCATION}/Active:/storage1/fs1/{$STORAGE_ALLOCATION}/Active" \
    thpc-batch bash -c "cd /path/to/nextflow/working/directory ; nextflow run nf-core/sarek -profile test -c /scratch1/fs1/ris/application/nextflow/conf/rnaseq.config --outdir /path/to/nextflow/working/directory"

- ``/path/to/nextflow/working/directory`` is the path to the Nextflow working directory.

Example Config File
-------------------

- The example config file below shows how the config file needs to be set up to interact with the Compute Platform

.. code::

    process {
        executor = "lsf"
        queue    = { "general" }
        clusterOptions =  { "-a 'docker(quay.io/${task.container})' -G compute-ris -J rnaseq -env 'all,PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'" }
    }

    executor {
        queueSize = 7
        submitRateLimit = '1/1sec'
    }