VG KMERS

Generates kmers from both strands of variation graphs.

Example

This wrapper can be used in the following way:

rule kmers:
    input:
        vgs="c.vg"
    output:
        kmers="kmers/c.kmers"
    params:
       "-gBk 16 -H 1000000000 -T 1000000001"
    log:
        "logs/vg/kmers/c.log"
    threads:
        4
    wrapper:
        "v1.9.0/bio/vg/kmers"

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

• vg==1.27.0

Authors

• Ali Ghaffaari

Code

__author__ = "Ali Ghaffaari"
__copyright__ = "Copyright 2017, Ali Ghaffaari"
__email__ = "ghaffari@mpi-inf.mpg.de"
__license__ = "MIT"


from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False)

shell(
    "(vg kmers {snakemake.params} --threads {snakemake.threads}"
    " {snakemake.input.vgs} > {snakemake.output.kmers}) {log}"
)