.. _`bio/gatk/printreadsspark`:

GATK PRINTREADSSPARK
====================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/gatk/printreadsspark?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/gatk/printreadsspark

Write reads from SAM format file (SAM/BAM/CRAM) that pass specified criteria to a new file. This is the version that can be run on Spark.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570521694747-PrintReadsSpark

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gatk_printreadsspark:
        input:
            bam="mapped/{sample}.bam",
            ref="genome.fasta",
            dict="genome.dict",
        output:
            bam="{sample}.bam",
        log:
            "logs/{sample}.log",
        params:
            extra="",  # optional
            java_opts="",  # optional
            #spark_runner="",  # optional, local by default
            #spark_v3.0.1="",  # optional
            #spark_extra="", # optional
        resources:
            mem_mb=1024,
        threads: 8
        wrapper:
            "v3.0.1/bio/gatk/printreadsspark"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Notes
-----

* The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
* The `extra` param allows for additional program arguments for `printreadsspark`.
* The `spark_runner` param = "LOCAL"|"SPARK"|"GCS" allows to set the spark_runner. Set the parameter to "LOCAL" or don't set it at all to run on local machine.
* The `spark_master` param allows to set the URL of the Spark Master to submit the job. Set to "local[number_of_cores]" for local execution. Don't set it at all for local execution with number of cores determined by snakemake.
* The `spark_extra` param allows for additional spark arguments.


Software dependencies
---------------------

* ``gatk4=4.4.0.0``
* ``snakemake-wrapper-utils=0.6.2``

Input/Output
------------
**Input:**

* bam file
* reference file
* reference dict

**Output:**

* filtered bam file




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2021, Filipe G. Vieira"
    __license__ = "MIT"

    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    extra = snakemake.params.get("extra", "")
    spark_runner = snakemake.params.get("spark_runner", "LOCAL")
    spark_master = snakemake.params.get(
        "spark_master", "local[{}]".format(snakemake.threads)
    )
    spark_extra = snakemake.params.get("spark_extra", "")
    java_opts = get_java_opts(snakemake)


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' PrintReadsSpark"
            " --input {snakemake.input.bam}"
            " --reference {snakemake.input.ref}"
            " {extra}"
            " --tmp-dir {tmpdir}"
            " --output {snakemake.output.bam}"
            " -- --spark-runner {spark_runner} --spark-master {spark_master} {spark_extra}"
            " {log}"
        )


.. |nl| raw:: html

   <br>