HOMER FINDPEAKS

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Find ChIP- or ATAC-Seq peaks with the HOMER suite. For more information, please see the documentation.

Example

This wrapper can be used in the following way:

rule homer_findPeaks:
    input:
        # tagDirectory of sample
        tag="tagDir/{sample}",
        # tagDirectory of control background sample - optional
        control="tagDir/control"
    output:
        "{sample}_peaks.txt"
    params:
        # one of 7 basic modes of operation, see homer manual
        style="histone",
        extra=""  # optional params, see homer manual
    log:
        "logs/findPeaks/{sample}.log"
    wrapper:
        "v3.10.2-32-gf4e5b66/bio/homer/findPeaks"

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)

control = snakemake.input.get("control", "")
if control == "":
    control_command = ""
else:
    control_command = "-i " + control

shell(
    "(findPeaks"
    " {snakemake.input.tag}"
    " -style {snakemake.params.style}"
    " {extra}"
    " {control_command}"
    " -o {snakemake.output})"
    " {log}"
)