.. _`bio/gatk/genomicsdbimport`:

GATK GENOMICSDBIMPORT
=====================


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

Run gatk GenomicsDBImport.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570326648475-GenomicsDBImport

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule genomics_db_import:
        input:
            gvcfs=["calls/a.g.vcf.gz", "calls/b.g.vcf.gz"],
        output:
            db=directory("db"),
        log:
            "logs/gatk/genomicsdbimport.log",
        params:
            intervals="ref",
            db_action="create",  # optional
            extra="",  # optional
            java_opts="",  # optional
        threads: 2
        resources:
            mem_mb=lambda wildcards, input: max([input.size_mb * 1.6, 200]),
        wrapper:
            "v3.0.1/bio/gatk/genomicsdbimport"

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 `intervals` param is mandatory
* By default, the wrapper will create a new database (output directory must be empty or non-existent). If you want to update an existing DB, set `db_action` param to `update`.
* The `extra` param allows for additional program arguments.


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

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

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

* GVCF files of multiple samples

**Output:**

* A GenomicsDB workspace




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

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


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


    extra = snakemake.params.get("extra", "")
    # uses Java native library TileDB, which requires a lot of memory outside
    # of the `-Xmx` memory, so we reserve 40% instead of the default 20%. See:
    # https://gatk.broadinstitute.org/hc/en-us/articles/9570326648475-GenomicsDBImportGenomicsDBImport
    java_opts = get_java_opts(snakemake, java_mem_overhead_factor=0.4)

    gvcfs = list(map("--variant {}".format, snakemake.input.gvcfs))

    db_action = snakemake.params.get("db_action", "create")
    if db_action == "create":
        db_action = "--genomicsdb-workspace-path"
    elif db_action == "update":
        db_action = "--genomicsdb-update-workspace-path"
    else:
        raise ValueError(
            "invalid option provided to 'params.db_action'; please choose either 'create' or 'update'."
        )

    intervals = snakemake.input.get("intervals")
    if not intervals:
        intervals = snakemake.params.get("intervals")

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

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' GenomicsDBImport"
            " --reader-threads {snakemake.threads}"
            " {gvcfs}"
            " --intervals {intervals}"
            " {extra}"
            " --tmp-dir {tmpdir}"
            " {db_action} {snakemake.output.db}"
            " {log}"
        )


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