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:
"0.74.0/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}"
)