.. _`bio/unicycler`:

UNICYCLER
=========


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

Assemble bacterial genomes with Unicycler.

You may find additional information on `Unicycler's <https://github.com/rrwick/Unicycler>`_ github page.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_unicycler:
        input:
            # R1 and R2 short reads:
            paired = expand(
                "reads/{sample}.{read}.fq.gz",
                read=["R1", "R2"],
                allow_missing=True
            )
            # Long reads:
            # long = long_reads/{sample}.fq.gz
            # Unpaired reads:
            # unpaired = reads/{sample}.fq.gz
        output:
            "result/{sample}/assembly.fasta"
        log:
            "logs/{sample}.log"
        params:
            extra=""
        wrapper:
            "v3.0.1/bio/unicycler"

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

* ``bowtie2=2.5.2``
* ``bcftools=1.18``
* ``spades=3.15.5``
* ``samtools=1.18``
* ``pilon=1.24``
* ``racon=1.5.0``
* ``blast=2.14.1``
* ``unicycler=0.5.0``

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

* Fastq-formatted reads

**Output:**

* Assembled reads




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    """Snakemake wrapper for Unicycler"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2020, Dayris Thibault"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from os.path import dirname
    from snakemake.shell import shell

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

    input_reads = ""
    if "paired" in snakemake.input.keys():
        input_reads += " --short1 {} --short2 {}".format(*snakemake.input.paired)
    if "unpaired" in snakemake.input.keys():
        input_reads += " --unpaired {} ".format(snakemake.input["unpaired"])
    if "long" in snakemake.input.keys():
        input_reads += " --long {} ".format(snakemake.input["long"])

    output_dir = " --out {} ".format(dirname(snakemake.output[0]))

    shell(
        " unicycler "
        " {input_reads} "
        " --threads {snakemake.threads} "
        " {output_dir} "
        " {extra} "
        " {log} "
    )


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