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:
"v2.6.0-35-g755343f/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
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}"
)