.. _`bio/purge_dups/ngscstat`:

PURGE_DUPS NGSCSTAT
===================


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

Purge haplotigs and overlaps in an assembly based on read depth

**URL**: https://github.com/dfguan/purge_dups

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule purge_dups_ngscstat:
        input:
            bam="reads.bam",
        output:
            cov="out/ngscstat.cov",
            stat="out/ngscstat.stat",
        log:
            "logs/ngscstat.log",
        params:
            extra="",
        threads: 1
        wrapper:
            "v3.0.1/bio/purge_dups/ngscstat"

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.


Notes
-----

* The `extra` param allows for additional program arguments.


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

* ``purge_dups=1.2.6``

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

* mapped reads in PAF format

**Output:**

* coverage
* stats




Authors
-------

* Filipe Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    import tempfile
    from snakemake.shell import shell


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


    with tempfile.TemporaryDirectory() as tmpdir:
        shell("ngscstat {extra} -O {tmpdir} {snakemake.input} {log}")

        if snakemake.output.get("cov"):
            shell("cat {tmpdir}/TX.base.cov > {snakemake.output.cov}")
        if snakemake.output.get("stat"):
            shell("cat {tmpdir}/TX.stat > {snakemake.output.stat}")


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