.. _`bio/assembly-stats`:

ASSEMBLY-STATS
==============


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

Generates report of summary statistics for a genome assembly

**URL**: https://github.com/sanger-pathogens/assembly-stats

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule run_assembly_stats:
        input:
            #Input assembly
            assembly="{sample}.fasta",
        output:
            #Assembly statistics
            assembly_stats="{sample}_stats.txt",
        params:
            # Tab delimited output, with a header, is set as the default. Other options are available:
            #   -l <int>
            #       Minimum length cutoff for each sequence.
            #       Sequences shorter than the cutoff will be ignored [1]
            #   -s
            #       Print 'grep friendly' output
            #   -t
            #       Print tab-delimited output
            #   -u
            #       Print tab-delimited output with no header line
            # If you want to add multiple options just delimit them with a space.
            # Note that you can only pick one output format
            # Check https://github.com/sanger-pathogens/assembly-stats for more details
            extra="-t",
        log:
            "logs/{sample}.assembly-stats.log",
        threads: 1
        wrapper:
            "v3.0.1/bio/assembly-stats"

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
-----

This tool/wrapper does not handle multi threading


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

* ``assembly-stats=1.0.1``

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

* ``assembly``: Genomic assembly (fasta format)

**Output:**

* ``assembly_stats``: Assembly statistics (format of your choosing, default = tab-delimited)



Params
------

* ``extra``: Optional parameters, see `assembly-stats official documentation <https://github.com/sanger-pathogens/assembly-stats#usage>`_




Authors
-------

* Pathogen Informatics, Wellcome Sanger Institute (assembly-stats tool) - https://github.com/sanger-pathogens
* Max Cummins (Snakemake wrapper [unaffiliated with Wellcome Sanger Institute])


Code
----

.. code-block:: python

    __author__ = "Max Cummins"
    __copyright__ = "Copyright 2021, Max Cummins"
    __email__ = "max.l.cummins@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell
    from os import path

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    shell(
        "assembly-stats"
        " {snakemake.params.extra}"
        " {snakemake.input.assembly}"
        " > {snakemake.output.assembly_stats}"
        " {log}"
    )


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