.. _`bio/genefuse`:

GENEFUSE
========


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

A tool to detect and visualize target gene fusions by scanning FASTQ files directly.

**URL**: https://github.com/OpenGene/GeneFuse

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule genefuse:
        input:
            fastq1="reads/{sample}_R1.fastq",
            fastq2="reads/{sample}_R2.fastq",
            config="genes.csv",
            reference="genome.fasta",
        output:
            html="{sample}_genefuse_report.html",
            json="{sample}_genefuse_report.json",
            fusions="{sample}_fusions.txt",
        log:
            "logs/{sample}_genefuse.log",
        params:
            # optional parameters
            extra="",
        threads:1
        wrapper:
            "v3.0.4/bio/genefuse"

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
-----

* The `extra` param allows for additional program arguments.


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

* ``genefuse=0.8.0``

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

* fastq files
* gene fuse settings files
* refeference genome

**Output:**

* txt file with fusions
* html report
* json report




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2022, Patrik Smeds"
    __email__ = "patrik.smeds@scilifelab.uu.se"
    __license__ = "MIT"


    from snakemake.shell import shell
    from tempfile import TemporaryDirectory

    # Formats the log redrection string
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    extra = snakemake.params.get("extra", "")

    with TemporaryDirectory() as tempdir:
        # Executed shell command
        html_path = f"{tempdir}/genefuse.html"
        json_path = f"{tempdir}/genefuse.json"
        txt_path = f"{tempdir}/gene_fuse_fusions.txt"
        shell(
            "(genefuse "
            "-r {snakemake.input.reference} "
            "-t {snakemake.threads} "
            "-f {snakemake.input.config} "
            "-1 {snakemake.input.fastq1} "
            "-2 {snakemake.input.fastq2} "
            "-h {html_path} "
            "-j {json_path} "
            "{extra} > "
            "{txt_path}) "
            "{log}"
        )

        if snakemake.output.get("html", None):
            shell("mv {html_path} {snakemake.output.html}")

        if snakemake.output.get("json", None):
            shell("mv {json_path} {snakemake.output.json}")

        if snakemake.output.get("fusions", None):
            shell("mv {txt_path} {snakemake.output.fusions}")


.. |nl| raw:: html

   <br>