VG PRUNE

Prunes the complex regions of the graph for GCSA2 indexing.

Example

This wrapper can be used in the following way:

rule prune:
    input:
        vg="c.vg"
    output:
        pruned="graph/c.pruned.vg"
    params:
        "-r"
    log:
        "logs/vg/prune/c.log"
    threads:
        4
    wrapper:
        "0.72.0/bio/vg/prune"

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 prune --threads {snakemake.threads} {snakemake.params}"
    " {snakemake.input.vg} > {snakemake.output.pruned}) {log}"
)