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.

URL:

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:
        "v1.1.0/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

Authors

• Jan Forster

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}")