.. _`bio/hap.py/pre.py`:

PRE.PY
======


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

Preprocessing/normalisation of vcf/bcf files. Part of the hap.py suite by Illumina (see https://github.com/Illumina/hap.py/blob/master/doc/normalisation.md).


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule preprocess_variants:
        input:
            ##vcf/bcf
            variants="variants.vcf",
        output:
            "normalized/variants.vcf.gz",
        log:
            "log/pre.log",
        params:
            ## path to reference genome
            genome="genome.fasta",
            ## parameters such as -L to left-align variants
            extra="-L",
        threads: 2
        wrapper:
            "v3.0.4/bio/hap.py/pre.py"

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
---------------------

* ``hap.py=0.3.15``




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster"
    __copyright__ = "Copyright 2019, Jan Forster"
    __email__ = "j.forster@dkfz.de"
    __license__ = "MIT"

    from os import path

    from snakemake.shell import shell

    ## Extract arguments
    extra = snakemake.params.get("extra", "")

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

    shell(
        "(pre.py"
        " --threads {snakemake.threads}"
        " -r {snakemake.params.genome}"
        " {extra}"
        " {snakemake.input.variants}"
        " {snakemake.output})"
        " {log}"
    )


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