.. _`utils/datavzrd`:

DATAVZRD
========


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   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Autils/datavzrd

datavzrd allows to render tables by providing a configuration file. 
Configuration templates can be dynamically customized by utilizing the 
`rendering integration <https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#template-rendering-integration>`_.
Any files specified in the configuration file have to be also specified as additional input files in the
datavzrd rule.


**URL**: https://github.com/datavzrd/datavzrd

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule datavzrd:
        input:
            config="resources/{sample}.datavzrd.yaml",
            # optional files required for rendering the given config
            table="data/{sample}.tsv",
        params:
            extra="",
        output:
            report(
                directory("results/datavzrd-report/{sample}"),
                htmlindex="index.html",
                # see https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html
                # for additional options like caption, categories and labels
            ),
        log:
            "logs/datavzrd_report/{sample}.log",
        wrapper:
            "v3.0.1/utils/datavzrd"

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

* ``datavzrd=2.31.0``




Authors
-------

* Felix Mölder


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2017, Johannes Köster"
    __email__ = "johannes.koester@protonmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell

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

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

    shell("datavzrd {snakemake.input.config} {extra} --output {snakemake.output[0]} {log}")


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