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:
        "v1.2.1/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}"
)