.. _sec-out:

====================================
Running the Pipeline and its Outputs
====================================

.. _run:

Starting a Run
--------------

Once ``run.yaml`` has been properly filled out, the pipeline can be 
launched (with an internet connection) with the following command:

::

   (psy-ngs) $ cd path/to/this/repo/
   (psy-ngs) $ python rkstr8_driver.py -p <pipeline-name> [ -a access_key_id ] [ -s secret_access_key ]

* ``pipeline-name`` can be either germline_wgs, or validation, to indicate whether or not the user wishes to run validation on GCP with Hail.
* ``access_key_id`` and ``secret_access_key`` are the access_key_id and secret_access_key key pair associated with the user's AWS account.

The pipeline initialization takes approximately 5 minutes.  
Afterwards, since the pipeline is serverless, the user can close their laptop 
(or similarily shut down their computer), and the pipeline will continue to run
on AWS.


---------------
Pipeline Output
---------------

For a given pipeline run, the user would have specified the ``OUTPUT`` field in
the ``run.yaml`` file.  All of the intermediate files and the final results of
the pipeline will be uploaded under the ``OUTPUT`` uri in the following scheme
if, for example, ``OUTPUT`` was set to ``s3://analysis/results/``:

.. code-block:: text
	
	aws s3 ls s3://analysis/results/
			PRE bam-processing/
			PRE bgz-gvcfs/
			PRE cohort-vcf-vqsr/
			PRE final-cohort-vcf/
			PRE logs/
			PRE processed-bams/

The figure below illustrates what files are written under which of the above
prefixes.

.. image:: PipelineWorkflowS3Locations.png

The **logs/** prefix contains the logs for all of the pipeline steps.