.. _nextflow_4-page:

*******************
4 Nextflow 
*******************

Modules and how to re-use the code
==================================

A great advantage of the Nextflow is to allow the **modularization of the code**.
In particular, you can move a named workflow within a module and keep it aside for being accessed by different pipelines.

The **test4** folder provides an example of using modules.

.. literalinclude:: ../nextflow/test4/test4.nf
   :language: groovy
   

We now include two modules, named **fastqc** and **multiqc**, from ```${projectDir}/modules/fastqc.nf``` and ```${projectDir}/modules/multiqc.nf```.
Let's inspect the **multiQC** module:

.. literalinclude:: ../nextflow/test4/modules/multiqc.nf
   :language: groovy


The module **multiqc** takes as **input** a channel with files containing reads and produces as **output** the files generated by the multiqc program.

The module contains the directive **publishDir**, the tag, and the container to be used and has a similar input, output, and script session as the fastqc process in **test3.nf**.

A module can have hardcoded information such as the label and the container, but you can also specify some of them via `nextflow.config`.


In this example, we have the hardcoded labels, output director, and label:

.. literalinclude:: ../nextflow/test4/modules/fastqc.nf
   :language: groovy
   :emphasize-lines: 8-10

In the multiqc module, we don't specify the container. We indicate it via `nextflow.config` file using the **withName** selector.

.. literalinclude:: ../nextflow/nextflow.config
   :language: groovy
   :emphasize-lines: 19-21,40-43,63-66


Here you see that we are not using our own image, but rather we use the image provided by **biocontainers** in `quay <://quay.io/>`__.

.. note::

	IMPORTANT: You have to specify a default image to run nextflow -with-docker or -with-singularity and you have to have a container(s) defined inside modules.


Reporting and graphical interface
===================================

Nextflow has an embedded function for reporting information about the resources requested for each job and the timing; to generate a html report, run Nextflow with the `-with-report` parameter :

.. code-block:: console

	nextflow run test5.nf -with-docker -bg -with-report > log


.. image:: images/report.png
  :width: 800


**Nextflow Seqera Platform (formerly known as Tower)** is an open-source monitoring and management platform for Nextflow workflows. There are two versions:

- Open source for monitoring of single pipelines.
- Commercial one for workflow management, monitoring, and resource optimization.

We will show the open-source one.

First, you need to access the `Seqera platform <://cloud.seqera.io/>`__ website and login.


.. image:: images/tower.png
  :width: 800

We recommend using either Google or GitHub for login. 

.. image:: images/tower0.png
  :width: 800

Once you are signed in you will see a page like this:

.. image:: images/tower2.png
  :width: 800


You can generate your token at `://cloud.seqera.io/tokens <://cloud.seqera.io/tokens>`__ and copy-paste it into your pipeline using this snippet in the configuration file:

.. code-block:: groovy

	tower {
	  accessToken = '<YOUR TOKEN>'
	  enabled = true
	}


or exporting those environmental variables:

.. code-block:: groovy

	export TOWER_ACCESS_TOKEN=*******YOUR***TOKEN*****HERE*******


Now we can launch the pipeline:

.. code-block:: console

	nextflow run test5.nf -with-singularity -with-tower -params-file params.yaml -bg > log


	CAPSULE: Downloading dependency io.nextflow:nf-tower:jar:20.09.1-edge
	CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:jar:3.0.5
	CAPSULE: Downloading dependency io.nextflow:nextflow:jar:20.09.1-edge
	CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:20.09.1-edge
	CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:jar:3.0.5
	CAPSULE: Downloading dependency org.codehaus.groovy:groovy:jar:3.0.5
	CAPSULE: Downloading dependency io.nextflow:nf-amazon:jar:20.09.1-edge
	CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:jar:3.0.5
	CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:jar:3.0.5


and go to the tower website again:


.. image:: images/tower3.png
  :width: 800


Once the pipeline is finished, you can also receive a mail.


.. image:: images/tower4.png
  :width: 800