BEDTOOLS SLOP¶
Increase the size of each feature in a BED/BAM/VCF by a specified factor.
URL:
Example¶
This wrapper can be used in the following way:
rule bedtools_merge:
input:
"A.bed"
output:
"A.slop.bed"
params:
## Genome file, tab-seperated file defining the length of every contig
genome="genome.txt",
## Add optional parameters
extra = "-b 10" ## in this example, we want to increase the feature by 10 bases to both sides
log:
"logs/slop/A.log"
wrapper:
"0.85.0/bio/bedtools/slop"
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¶
bedtools=2.29.0
Authors¶
- Jan Forster
Code¶
__author__ = "Jan Forster"
__copyright__ = "Copyright 2019, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"
from snakemake.shell import shell
## Extract arguments
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"(bedtools slop"
" {extra}"
" -i {snakemake.input[0]}"
" -g {snakemake.params.genome}"
" > {snakemake.output})"
" {log}"
)