.. _`bio/galah`:

GALAH
=====


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

More scalable dereplication for metagenome assembled genomes

**URL**: https://github.com/wwood/galah

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule galah_fas:
        input:
            fas=["fas/a.fa", "fas/b.fas.bz2", "fas/c.fasta.gz"],
        output:
            clusters="results.fas.tsv",
            repres="results.fas.list",
        log:
            "logs/out.fas.log",
        params:
            extra="--precluster-ani 0.9 --ani 0.95",
        threads: 2
        resources:
            mem_mb=50,
        wrapper:
            "v3.0.1/bio/galah"


    use rule galah_fas as galah_fas_list with:
        input:
            fas_list="fas/a.fas_list",
        output:
            clusters="results.fas_list.tsv",
            repres="results.fas_list.list",
        log:
            "logs/out.fas_list.log",

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

* ``galah=0.3.1``

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

* FASTA files

**Output:**

* ``clusters``: representative FASTA<TAB>member lines
* ``repres``: paths to representative FAS files



Params
------

* ``extra``: additional program arguments




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2023, Filipe G. Vieira"
    __license__ = "MIT"

    from snakemake.shell import shell


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


    fas = snakemake.input.get("fas", "")
    if fas:
        fas = f"--genome-fasta-files {' '.join(fas)}"


    fas_list = snakemake.input.get("fas_list", "")
    if fas_list:
        fas_list = f"--genome-fasta-list {fas_list}"


    clusters = snakemake.output.get("clusters", "")
    if clusters:
        clusters = f"--output-cluster-definition {clusters}"


    repres = snakemake.output.get("repres", "")
    if repres:
        repres = f"--output-representative-list {repres}"


    shell(
        "galah cluster"
        " --threads {snakemake.threads}"
        " {fas}"
        " {fas_list}"
        " {extra}"
        " {clusters}"
        " {repres}"
        " {log}"
    )


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