.. _`bio/purge_dups/purge_dups`:

PURGE_DUPS
==========


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

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:
        input:
            paf="split.self.paf.gz",
            #cov="pbcstat.cov",
            #cutoff="calcuts.cutoffs",
        output:
            "out/purge_dups.bed",
        log:
            "logs/purge_dups.log",
        params:
            extra="-2",
        threads: 1
        wrapper:
            "v3.0.1/bio/purge_dups/purge_dups"

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:**

* Self-aligned split assembly in PAF format

**Output:**

* BED file




Authors
-------

* Filipe Vieira


Code
----

.. code-block:: python

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


    from snakemake.shell import shell


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


    cov = snakemake.input.get("cov", "")
    if cov:
        cov = f"-c {cov}"

    cutoff = snakemake.input.get("cutoff", "")
    if cutoff:
        cutoff = f"-T {cutoff}"


    shell(
        "purge_dups {cov} {cutoff} {extra} {snakemake.input.paf} > {snakemake.output[0]} {log}"
    )


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