REFGENIE

Deploy biomedical reference datasets via refgenie.

URL: https://refgenie.databio.org/en/latest/

Example

This wrapper can be used in the following way:

rule obtain_asset:
    output:
        # the name refers to the refgenie seek key (see attributes on http://refgenomes.databio.org)
        fai="refs/genome.fasta"
        # Multiple outputs/seek keys are possible here.
    params:
        genome="human_alu",
        asset="fasta",
        tag="default"
    wrapper:
        "v9.5.0/bio/refgenie"

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

• refgenie=0.13.0

• refgenconf=0.13.1

Authors

• Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2019, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"

import os
import refgenconf

conf_path = os.environ["REFGENIE"]

rgc = refgenconf.RefGenConf.from_yaml_file(conf_path)

# pull asset if necessary
gat, archive_data, server_url = rgc.pull(
    snakemake.params.genome, snakemake.params.asset, snakemake.params.tag, force=False
)

for seek_key, out in snakemake.output.items():
    path = rgc.seek(
        snakemake.params.genome,
        snakemake.params.asset,
        tag_name=snakemake.params.tag,
        seek_key=seek_key,
        strict_exists=True,
    )
    os.symlink(path, out)