VG PRUNE¶
Prunes the complex regions of the graph for GCSA2 indexing.
URL:
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:
"v0.80.1/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}"
)