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:

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:
        "v1.25.0-52-g79342b73/bio/genefuse"

Note that input, output and log file paths can be chosen freely.

When running with

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

__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}")