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Running Nextflow pipeline on public BAM file from ISB-CGC
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This Nextflow workflow gathers GC content from a BAM file (or a list of BAM files) to a text file. 
By using software containers, `Nextflow <https://www.nextflow.io>`_ enables scalable and reproducible scientific workflows. Pipelines can be written in the most common scripting languages.


Requirements:
=============

- Docker
- Java (required to install Nextflow)
- Gcsfuse
- Nextflow
- A public bam file from ISB-CGC at the address: gs://gdc-ccle-open/692a845c-7957-41f2-b679-5434c69ba25b/G27328.Calu-6.1.bam

To install Docker and Nextflow, see our `VM Workflow Tools Installation Cheatsheet <Cheatsheet.html>`_ for instructions. To set up gcsfuse in order to get access to the BAM file, please visit `Running Workflow with GCSFUSE <WorkflowWithGCSFUSE.html>`_.


.. note:: The requirements above are crucial to running this workflow. Please make sure you have them installed properly prior to running this workflow.



Download this tutorial:
=======================
::

 $ sudo add-apt-repository universe
 $ sudo apt update
 $ sudo apt install subversion

 #cloning this tutorial
 $ svn checkout https://github.com/isb-cgc/RunningWorkflows-on-the-GoogleCloud/trunk/Nextflow-GCgather

Running Nextflow
================
  You should have a **Nextflow-GCgather** directory with one file called **Nextflow-GCgather.nf** inside. We are going to change the address in this file to the one you created in the **Running Workflow with GCSFUSE** tutorial.

::

  #go into the folder
  $ cd Nextflow-GCgather
  $ nano Nextflow-GCgather.nf

At the top of the file you will see this:

::

  #!/usr/bin/env nextflow
  myBamSample = Channel.fromPath('/home/thinh_vo/sample/*.bam')


Replace "/home/thinh_vo/sample/\*.bam" with your new address from the gcsfuse tutorial for example: "/home/thinh_vo/testGcsfuse/\*.bam". Now the script is ready to run with Nextflow.

::

  #Go to where the Nextflow executable file was installed in this example. It will be outside the Nextflow-GCgather directory.
  #First, we get out of Nextflow-GCgather directory.
  $ cd ..
  #execute nextflow with docker image:
  $ ./nextflow run Nextflow-GCgather/Nextflow-GCgather.nf -with-docker gcr.io/genomics-tools/samtools

.. note:: This BAM file is quite large; it may take about 15 mins ~ 20 mins to run.

Once Nextflow is finished, the result will be on the screen, or you can find it at **Nextflow-GCgather/Sam_results/final_gc_stats_out.txt**.

Running Nextflow with visualization
-----------------------------------
You can use this command instead to run Nextflow; it will out put a visualization file named "flowchart.png".


::

  $ ./nextflow run Nextflow-GCgather/Nextflow-GCgather.nf -with-dag flowchart.png


It should look like this:

  .. image:: images/RunningNextflowWithBam.png
     :align: center

To see the result of this workflow, you can check it `here <https://github.com/isb-cgc/RunningWorkflows-on-the-GoogleCloud/tree/master/Results/GC-gather>`_.