HOMER MAKETAGDIRECTORY
Create a tag directory with the HOMER suite. For more information, please see the documentation.
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:
"v5.0.1/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.
Software dependencies
homer=4.11
samtools=1.21
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}"
)