VG CONSTRUCT
Construct variation graphs from a reference and variant calls.
Example
This wrapper can be used in the following way:
rule construct:
input:
ref="c.fa",
vcfgz="c.vcf.gz"
output:
vg="graph/c.vg"
params:
"--node-max 10"
log:
"logs/vg/construct/c.log"
threads:
4
wrapper:
"v5.8.0/bio/vg/construct"
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=1.63.1
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 construct {snakemake.params} --reference {snakemake.input.ref}"
" --vcf {snakemake.input.vcfgz} --threads {snakemake.threads}"
" > {snakemake.output.vg}) {log}"
)