.. _`bio/ragtag/scaffold`:

RAGTAG-SCAFFOLD
===============


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

Homology-based assembly scaffolding.

**URL**: https://github.com/malonge/RagTag/wiki/scaffold

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule scaffold:
        input:
            query="fasta/{query}.fasta",
            ref="fasta/{reference}.fasta",
        output:
            fasta="{query}_scaffold_{reference}/ragtag.scaffold.fasta",
            agp="{query}_scaffold_{reference}/ragtag.scaffold.agp",
            stats="{query}_scaffold_{reference}/ragtag.scaffold.stats",
        params:
            extra="",
        threads: 16
        log:
            "logs/ragtag/{query}_scaffold_{reference}.log",
        wrapper:
            "v3.0.1/bio/ragtag/scaffold"

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
-----

Multiple threads can be used during Minimap/Unimap alignment.

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

* ``ragtag=2.1.0``

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

* ``ref``: reference fasta file (uncompressed or bgzipped)
* ``query``: query fasta file (uncompressed or bgzipped)

**Output:**

* ``fasta``: The scaffolds in FASTA format, defined by the ordering and orientations of ragtag.scaffold.agp.
* ``agp``: The ordering and orientations of query sequences in AGP format.
* ``stats``: Summary statistics for the scaffolding process.



Params
------

* ``extra``: additional parameters




Authors
-------

* Curro Campuzano Jiménez


Code
----

.. code-block:: python

    """Snakemake wrapper for ragtag-scaffold."""

    __author__ = "Curro Campuzano Jiménez"
    __copyright__ = "Copyright 2023, Curro Campuzano Jiménez"
    __email__ = "campuzanocurro@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell
    import tempfile

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

    assert snakemake.output.keys(), "Output must contain at least one named file."

    valid_keys = ["agp", "fasta", "stats"]
    for key in snakemake.output.keys():
        assert (
            key in valid_keys
        ), "Invalid key in output. Valid keys are: %r. Given: %r." % (valid_keys, key)

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "ragtag.py scaffold"
            " {snakemake.input.ref}"
            " {snakemake.input.query}"
            " {extra}"
            " -o {tmpdir} -t {snakemake.threads}"
            " {log}"
        )

        for key in valid_keys:
            outfile = snakemake.output.get(key)
            if outfile:
                shell("mv {tmpdir}/ragtag.scaffold.{key} {outfile}")


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