WGSIM

Short read simulator.

Example

This wrapper can be used in the following way:

rule wgsim:
    input:
        ref="genome.fa"
    output:
        read1="reads/1.fq",
        read2="reads/2.fq"
    log:
        "logs/wgsim/sim.log"
    params:
        "-X 0 -R 0 -r 0.1 -h"
    wrapper:
        "0.75.0-11-g981b16b/bio/wgsim"

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

  • wgsim==1.0.0

Authors

  • Ali Ghaffaari

Code

__author__ = "Ali Ghaffaari"
__copyright__ = "Copyright 2018, Ali Ghaffaari"
__email__ = "ali.ghaffaari@mpi-inf.mpg.de"
__license__ = "MIT"


from snakemake.shell import shell

log = snakemake.log_fmt_shell()

shell(
    "(wgsim {snakemake.params} {snakemake.input.ref}"
    " {snakemake.output.read1} {snakemake.output.read2}) {log}"
)