.. _`bio/optitype`:

OPTITYPE
========


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

Precision 4-digit HLA-I-typing from NGS data based on integer linear programming. Use razers3 beforehand to generate input fastq files only mapping to HLA-regions. Please see https://github.com/FRED-2/OptiType


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule optitype:
        input:
            # list of input reads
            reads=["reads/{sample}_1.fished.fastq", "reads/{sample}_2.fished.fastq"]
        output:
            pdf="optitype/{sample}_coverage_plot.pdf",
            tsv="optitype/{sample}_result.tsv",
        log:
            "logs/optitype/{sample}.log"
        params:
            # Type of sequencing data. Can be 'dna' or 'rna'. Default is 'dna'.
            sequencing_type="dna",
            # optiype config file, optional
            config="",
            # additional parameters
            extra=""
        wrapper:
            "v3.0.1/bio/optitype"

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.


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

* ``optitype=1.3.5``




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster, David Lähnemann"
    __copyright__ = "Copyright 2020, Jan Forster"
    __email__ = "j.forster@dkfz.de"
    __license__ = "MIT"


    import os
    from tempfile import TemporaryDirectory
    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    # get sequencing type
    seq_type = snakemake.params.get("sequencing_type", "dna")
    seq_type = "--{}".format(seq_type)

    # check if non-default config.ini is used
    config = snakemake.params.get("config", "")
    if any(config):
        config = "--config {}".format(config)

    with TemporaryDirectory() as tempdir:
        shell(
            "(OptiTypePipeline.py"
            "  --input {snakemake.input.reads}"
            "  --outdir {tempdir}"
            "  --prefix tmp_prefix"
            "  {seq_type}"
            "  {config}"
            "  {extra}; "
            " mv {tempdir}/tmp_prefix_coverage_plot.pdf {snakemake.output.pdf:q} ;"
            " mv {tempdir}/tmp_prefix_result.tsv {snakemake.output.tsv:q} )"
            " {log}"
        )


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