MINIMAP2 INDEX

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/minimap2/index?label=version%20update%20pull%20requests

creates a minimap2 index

URL: https://lh3.github.io/minimap2

Example

This wrapper can be used in the following way:

rule minimap2_index:
    input:
        target="target/{input1}.fasta"
    output:
        "{input1}.mmi"
    log:
        "logs/minimap2_index/{input1}.log"
    params:
        extra=""  # optional additional args
    threads: 3
    wrapper:
        "v3.8.0-49-g6f33607/bio/minimap2/index"

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

  • minimap2=2.28

Input/Output

Input:

  • reference genome in FASTA format

Output:

  • indexed reference genome

Authors

  • Tom Poorten

Code

__author__ = "Tom Poorten"
__copyright__ = "Copyright 2017, Tom Poorten"
__email__ = "tom.poorten@gmail.com"
__license__ = "MIT"

from snakemake.shell import shell

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

shell(
    "(minimap2 -t {snakemake.threads} {extra} "
    "-d {snakemake.output[0]} {snakemake.input.target}) {log}"
)