.. _`bio/benchmark/chm-eval-kit`:

CHM-EVAL-KIT
============


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

Download CHM-eval kit for benchmarking variant calling.

**URL**: https://github.com/lh3/CHM-eval

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule chm_eval_kit:
        output:
            directory("resources/chm-eval-kit"),
        params:
            # Tag and version must match, see https://github.com/lh3/CHM-eval/releases.
            tag="v0.5",
            version="20180222",
        log:
            "logs/chm-eval-kit.log",
        cache: "omit-software"
        wrapper:
            "v3.0.1/bio/benchmark/chm-eval-kit"

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

* ``curl``



Params
------

* ``tag``: Release tag, see git official repository

* ``version``: Release version, see git official repository




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2020, Johannes Köster"
    __email__ = "johannes.koester@uni-due.de"
    __license__ = "MIT"

    import os
    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    url = (
        "https://github.com/lh3/CHM-eval/releases/"
        "download/{tag}/CHM-evalkit-{version}.tar"
    ).format(version=snakemake.params.version, tag=snakemake.params.tag)

    os.makedirs(snakemake.output[0])
    shell(
        "(curl -L {url} | tar --strip-components 1 -C {snakemake.output[0]} -xf - &&"
        "(cd {snakemake.output[0]}; chmod +x htsbox run-eval k8)) {log}"
    )


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