.. _`bio/shovill`:

SHOVILL
=======


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

Assemble bacterial isolate genomes from Illumina paired-end reads.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule shovill:
      input:
        r1="reads/{sample}_R1.fq.gz",
        r2="reads/{sample}_R2.fq.gz"
      output:
        raw_assembly="assembly/{sample}.{assembler}.assembly.fa",
        contigs="assembly/{sample}.{assembler}.contigs.fa"
      params:
        extra=""
      log:
        "logs/shovill/{sample}.{assembler}.log"
      threads: 1
      wrapper:
        "v3.0.1/bio/shovill"

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

* ``shovill=1.1.0``




Authors
-------

* Sangram Keshari Sahu


Code
----

.. code-block:: python

    """Snakemake wrapper for shovill."""

    __author__ = "Sangram Keshari Sahu"
    __copyright__ = "Copyright 2020, Sangram Keshari Sahu"
    __email__ = "sangramsahu15@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell
    from tempfile import TemporaryDirectory

    # Placeholder for optional parameters
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    params = snakemake.params.get("extra", "")

    with TemporaryDirectory() as tempdir:
        shell(
            "(shovill"
            " --assembler {snakemake.wildcards.assembler}"
            " --outdir {tempdir} --force"
            " --R1 {snakemake.input.r1}"
            " --R2 {snakemake.input.r2}"
            " --cpus {snakemake.threads}"
            " {params}) {log}"
        )

        shell(
            "mv {tempdir}/{snakemake.wildcards.assembler}.fasta {snakemake.output.raw_assembly}"
            " && mv {tempdir}/contigs.fa {snakemake.output.contigs}"
        )


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