HOMER MERGEPEAKS
Merge ChIP-Seq peaks from multiple peak files. For more information, please see the documentation. Please be aware that this wrapper does not yet support use of the -prefix
parameter.
Example
This wrapper can be used in the following way:
rule homer_mergePeaks:
input:
# input peak files
"peaks/{sample1}.peaks",
"peaks/{sample2}.peaks"
output:
"merged/{sample1}_{sample2}.peaks"
params:
extra="-d given" # optional params, see homer manual
log:
"logs/mergePeaks/{sample1}_{sample2}.log"
wrapper:
"v5.0.0/bio/homer/mergePeaks"
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
homer=4.11
Code
__author__ = "Jan Forster"
__copyright__ = "Copyright 2020, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"
from snakemake.shell import shell
import os.path as path
import sys
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
class PrefixNotSupportedError(Exception):
pass
if "-prefix" in extra:
raise PrefixNotSupportedError(
"The use of the -prefix parameter is not yet supported in this wrapper"
)
shell("(mergePeaks" " {snakemake.input}" " {extra}" " > {snakemake.output})" " {log}")