MINIMAP2 INDEX

creates a minimap2 index

Software dependencies

  • minimap2 ==2.5

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:
        "0.20.1/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.

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}")