GFF3

Tool to parse, possibly transform, and output GFF3 files

URL: https://github.com/genometools/genometools

Example

This wrapper can be used in the following way:

rule genometools_gff3:
    input:
        "{sample}.gff3",
    output:
        "{sample}.revised.gff3",
    log:
        "logs/genometools/gff3/{sample}.log",
    params:
        extra="",
    wrapper:
        "v9.4.0/bio/genometools/gff3"

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.

Software dependencies

• genometools-genometools=1.6.6

Input/Output

Input:

• GFF3 file

Output:

• output GFF3 file

Params

• extra: additional program arguments.

Authors

• Jorge Alvarez-Jarreta

Code

__author__ = "Jorge Alvarez-Jarreta"
__copyright__ = "Copyright 2026, Jorge Alvarez-Jarreta"
__mail__ = "jalvarez@ebi.ac.uk"
__license__ = "Apache License 2.0"


from snakemake.shell import shell

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

shell("gt gff3 {extra} -o {snakemake.output[0]} {snakemake.input[0]} {log}")