.. _`bio/vembrane/table`:

VEMBRANE TABLE
==============


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

Vembrane table allows to generate table-like textfiles from vcfs based on any INFO field, CHROM, POS, REF, ALT, QUAL, and the annotation field ANN. When filtering based on ANN, annotation entries are filtered first. https://github.com/vembrane/vembrane


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule vembrane_table:
        input:
            vcf="in.vcf",
        output:
            vcf="table/out.tsv"
        params:
            expression="CHROM, POS, ALT, REF",
            extra=""
        log:
            "logs/vembrane.log"
        wrapper:
            "v3.0.1/bio/vembrane/table"

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

* ``vembrane=1.0.3``

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

* A VCF-formatted file

**Output:**

* A table-like textfile




Authors
-------

* Christopher Schröder


Code
----

.. code-block:: python

    """Snakemake wrapper for vembrane"""

    __author__ = "Christopher Schröder"
    __copyright__ = "Copyright 2020, Christopher Schröder"
    __email__ = "christopher.schroeder@tu-dortmund.de"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    extra = snakemake.params.get("extra", "")

    shell(
        "vembrane table"  # Tool and its subcommand
        " {extra}"  # Extra parameters
        " {snakemake.params.expression:q}"
        " {snakemake.input}"  # Path to input file
        " > {snakemake.output}"  # Path to output file
        " {log}"  # Logging behaviour
    )


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