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Working Examples
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All these working examples demonstrate prefered ways to solve some of the common problems encountered when developing WDLs. These examples are not really meaningful for non-WDL developers.

.. role:: listsize
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.. warning::
    Remember to have the jaws environment activated. See :doc:`Set up JAWS Environment </jaws/jaws_quickstart>`


How to Run an Example
---------------------
To run the following examples, click on an example link and clone the repo. For the subworkflow example, you would do:

.. code-block:: text

    git clone https://code.jgi.doe.gov/official-jgi-workflows/wdl-specific-repositories/jaws-tutorial-examples.git

    # If you clicked on the subworkflow link below, you can see the directory name is subworkflows_and_conditionals 
    cd subworkflows_and_conditionals

And then follow the command in the README.md of that example.

.. code-block:: text
    
    jaws submit main.wdl inputs.json dori


Examples
------------

.. dropdown:: Subworkflows
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    Simplest example

    `alignment example <https://code.jgi.doe.gov/official-jgi-workflows/wdl-specific-repositories/jaws-tutorial-examples/tree/master/jaws-alignment-example>`_ 

    Conditionals determining which subworkflow to run

    `subworkflows_and_conditionals <https://code.jgi.doe.gov/official-jgi-workflows/wdl-specific-repositories/jaws-tutorial-examples/tree/master/subworkflows_and_conditionals>`_   

    Importing subworkflows by URL

    `subworkflow_remote_subs <https://code.jgi.doe.gov/official-jgi-workflows/wdl-specific-repositories/jaws-tutorial-examples/tree/master/subworkflow_remote_subs>`_
    

.. dropdown:: Scattering
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    Scattering is the prefered way to run jobs in parallel. "Scatter-gathering" represents the parallization of jobs and the subsequent combining of results into one array for downstream usage.

    `scattering <https://code.jgi.doe.gov/official-jgi-workflows/wdl-specific-repositories/jaws-tutorial-examples/tree/master/scatter_gather_example>`_ 
    
.. dropdown:: Sharding
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    "Sharding" is the term used for splitting a file (like fasta, fastq, txt, etc.) into pieces that can then be processed in parallel. 

    `sharding input files <https://code.jgi.doe.gov/official-jgi-workflows/wdl-specific-repositories/jaws-tutorial-examples/tree/master/jaws-sharding>`_ 
    
.. dropdown:: Using Refdata
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    Here is an example of how to use a database (e.g. for blast) within your WDL so that you don't have to make a copy of it everytime you submit the WDL. Your reference files can be put into a directory dedicated to them on `/global/dna/shared/databases/<your-username>` on perlmutter. When you run a WDL, the keyword `/refdata` can be used within the commands section to access your refdata files.  This works because `/refdata` is mounted into the docker container and points to your refdata files no matter which compute site you are using since the files get synced nightly.

    `using reference databases <https://code.jgi.doe.gov/official-jgi-workflows/wdl-specific-repositories/jaws-tutorial-examples/tree/master/referencing_db_and_shifter>`_ 

.. dropdown:: Custom Data Structure
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    Here is an example of creating your own datastructure, i.e. instead of using the pre-defined ones like "String, Int, Array, Map, etc." This may be useful to use for input that you want organized in a certain way. For more info, see the official documentation `spec1.0 <https://github.com/openwdl/wdl/blob/legacy/versions/1.0/SPEC.md#struct-definition>`_

    `using datastructure for reference data <https://code.jgi.doe.gov/official-jgi-workflows/wdl-specific-repositories/jaws-tutorial-examples/tree/master/using_ref_datastructure>`_

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Additional links
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Real world general examples 

    * `biowdl <https://github.com/biowdl>`_

    * `dockstore.org <https://dockstore.org/search?_type=workflow&descriptorType=wdl&descriptorType=WDL&searchMode=files>`_