.. role:: chocolate

Welcome to JAWS
---------------

.. figure:: /Figures/JAWS_2.png
    :scale: 100%

Overview
--------

JAWS (JGI Analysis Workflow Service) is a scalable and centralized workflow execution framework developed by the `DOE Joint Genome Institute <https://jgi.doe.gov>`_ (JGI). 
It enables researchers to efficiently run complex computational workflows across multiple high-performance computing (HPC) resources.
JAWS automates resource configuration, data transfer, and job scheduling, allowing users to focus on their scientific tasks while ensuring workflow reproducibility and scalability.

Key Features
------------

- **Multi-Site Workflow Management:** JAWS orchestrates workflows across multiple sites, including `LabIT <https://scienceit-docs.lbl.gov/hpc/>`_, `NERSC <https://www.nersc.gov/>`_, `EMSL <https://www.emsl.pnnl.gov/MSC/UserGuide/index.html>`_, and expanding to `ALCF <https://www.alcf.anl.gov/>`_ (Crux) and `OLCF <https://www.olcf.ornl.gov/>`_ (Defiant).

- **User-Friendly CLI and Python Library**: The JAWS Client provides a lightweight and efficient command-line interface (CLI) and Python library for seamless workflow submission, monitoring, and retrieval of results.

- **Leverages Community-Supported Tools**: Uses `Cromwell <https://cromwell.readthedocs.io/en/stable/>`_, `Workflow Description Language (WDL) <https://github.com/openwdl/wdl/blob/legacy/versions/1.0/SPEC.md>`_, `HTCondor <https://htcondor.org/>`_, and containerization technologies like `Apptainer <https://apptainer.org/>`_ and `Shifter <https://docs.nersc.gov/development/containers/shifter/>`_.

- **Data Transfer & Security**: Integrates `Globus <https://www.globus.org/>`_ for secure and efficient data movement.

- **User Support & Engagement**: Regular user meetings, workshops, and dedicated office hours.

- **Performance Monitoring**: JAWS is integrated with Elasticsearch and Kibana to track job performance metrics, providing users with execution insights and efficiency.


Getting Started with JAWS
-------------------------

New to JAWS? Start by exploring:

- :doc:`Why JAWS <Intro/why_jaws>`

- :doc:`How JAWS Works <Intro/how_jaws>`

- :doc:`Installation & Setup <jaws/jaws_config>`

Ready to start? Whether you're writing your own workflows or running existing ones, here's how to dive in:

- :doc:`Build Your Own WDL <Tutorials/building_wdls>`: Learn how to create workflows using WDL, with tips and best practices for building robust and scalable pipelines.
- :doc:`Run an Existing WDL in JAWS <jaws/jaws_quickstart>`: Start executing workflows with JAWS by following this quickstart guide.


.. toctree::
   :hidden:
   :name: extradoc
   :maxdepth: 1
   :caption: Intro

   How JAWS Works <Intro/how_jaws>
   Why use JAWS <Intro/why_jaws>
   JAWS Video Library<Intro/videos>
   Getting Help <Intro/contact_us>
   FAQ <Intro/faq>

.. toctree::
   :hidden:
   :name: getstarted
   :maxdepth: 2
   :caption: JAWS

   Configuring the JAWS Client <jaws/jaws_config>
   Quickstart Example <jaws/jaws_quickstart>
   JAWS Commands <jaws/jaws_usage>
   JAWS Python Libray <jaws/jaws_python.rst>
   JAWS Teams <jaws/jaws_teams>
   JAWS Performance Metrics <jaws/jaws_perf_metrics>
   JAWS Notifications <jaws/jaws_notification>
   JAWS Fair-share Policies <jaws/jaws_policies.rst>
   JAWS Guidelines <jaws/jaws_guide.rst>
   JAWS Backend <jaws/jaws_backend.rst>
   JAWS Refdata <jaws/jaws_refdata.rst>
   JAWS Troubleshooting <jaws/jaws_troubleshooting>

.. toctree::
   :hidden:
   :name: specsdoc
   :maxdepth: 1
   :caption: General Resources

   Compute Resources <Resources/compute_resources.rst>
   Cromwell <Specifications/cromwell>
   Best Practices for WDLs <Resources/best_practices>
   Working Examples <Tutorials/example_wdls>
   JGI Subworkflows and Tasks <Resources/subworkflows>
   Installing MySQL for Cromwell <Specifications/mysql_for_cromwell.rst>

.. toctree::
   :hidden:
   :name: wdldevelop
   :maxdepth: 3
   :caption: Tutorials
   
   Lesson 1: Development Environment <Tutorials/wdl_development>
   Lesson 2: Create Docker Container <Tutorials/create_env>
   Lesson 3: Write a WDL <Tutorials/building_wdls>
   Lesson 4: Defining the Input Data <Tutorials/inputs_json>

.. toctree::
   :hidden:
   :name: release
   :maxdepth: 3
   :caption: JAWS Release 

   JAWS Release Notes <Release/release_notes>

.. toctree::
   :hidden:
   :name: training
   :maxdepth: 2
   :caption: JAWS Events

   Upcoming JAWS Events <training/upcoming-workshop>
   JAWS Events Archive <training/archive>

.. toctree::
   :hidden:
   :name: extras
   :maxdepth: 3
   :caption: Extra Links

   Tutorial for Testing WDLs with Pytest <Tutorials/extras>