BISMARK_GENOME_PREPARATION
Generate indexes for Bismark (see https://github.com/FelixKrueger/Bismark/blob/master/bismark_genome_preparation).
Example
This wrapper can be used in the following way:
# For *.fa file
rule bismark_genome_preparation_fa:
input:
"indexes/{genome}/{genome}.fa"
output:
directory("indexes/{genome}/Bisulfite_Genome")
log:
"logs/indexes/{genome}/Bisulfite_Genome.log"
params:
"" # optional params string
wrapper:
"v5.8.0/bio/bismark/bismark_genome_preparation"
# Fo *.fa.gz file:
rule bismark_genome_preparation_fa_gz:
input:
"indexes/{genome}/{genome}.fa.gz"
output:
directory("indexes/{genome}/Bisulfite_Genome")
log:
"logs/indexes/{genome}/Bisulfite_Genome.log"
params:
extra="" # optional params string
wrapper:
"v5.8.0/bio/bismark/bismark_genome_preparation"
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
bowtie2=2.5.4
bismark=0.24.2
samtools=1.21
Input/Output
Input:
path to genome *.fa (or *.fasta, *.fa.gz, *.fasta.gz) file
Output:
No ouptut, generates bismark indexes in parent directory of input file
Code
"""Snakemake wrapper for Bismark indexes preparing using bismark_genome_preparation."""
# https://github.com/FelixKrueger/Bismark/blob/master/bismark_genome_preparation
__author__ = "Roman Chernyatchik"
__copyright__ = "Copyright (c) 2019 JetBrains"
__email__ = "roman.chernyatchik@jetbrains.com"
__license__ = "MIT"
from os import path
from snakemake.shell import shell
input_dir = path.dirname(snakemake.input[0])
params_extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell("bismark_genome_preparation --verbose --bowtie2 {params_extra} {input_dir} {log}")