VG INDEX GCSA

Build GCSA index for variation graphs.

Example

This wrapper can be used in the following way:

rule gcsa:
    input:
        vgs=["x.vg", "c.vg"]
    output:
        gcsa="index/wg.gcsa"
    params:
        "-Z 3000 -X 3"
    log:
        "logs/vg/index/gcsa/wg.log"
    threads:
        4
    wrapper:
        "0.72.0/bio/vg/index/gcsa"

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()

shell(
    "(vg index -g {snakemake.output.gcsa} --threads {snakemake.threads}"
    " {snakemake.params} {snakemake.input.vgs}) {log}"
)