HOMER MAKETAGDIRECTORY

Create a tag directory with the HOMER suite. For more information, please see the documentation.

Software dependencies

  • homer ==4.11
  • samtools ==1.10

Example

This wrapper can be used in the following way:

rule homer_makeTagDir:
    input:
        # input bam, can be one or a list of files
        bam="{sample}.bam",
    output:
        directory("tagDir/{sample}")
    params:
        extra=""  # optional params, see homer manual
    log:
        "logs/makeTagDir/{sample}.log"
    wrapper:
        "0.65.0/bio/homer/makeTagDirectory"

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.

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)

shell(
    "(makeTagDirectory" " {snakemake.output}" " {extra}" " {snakemake.input})" " {log}"
)