VG MERGE¶
Generate a joint id space across each graph and merge them all.
URL:
Example¶
This wrapper can be used in the following way:
rule merge:
input:
vgs=["c.vg", "x.vg"]
output:
merged="graph/wg.vg"
log:
"logs/vg/merge/wg.log"
wrapper:
"0.85.0/bio/vg/merge"
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 ids --join {snakemake.input.vgs} &&"
" for VGFILE in {snakemake.input.vgs};"
" do cat $VGFILE >> {snakemake.output.merged};"
" done) {log}"
)