BOWTIE2_BUILD¶
Map reads with bowtie2.
Example¶
This wrapper can be used in the following way:
rule bowtie2_build:
input:
reference="genome.fasta"
output:
multiext(
"genome",
".1.bt2", ".2.bt2", ".3.bt2", ".4.bt2", ".rev.1.bt2", ".rev.2.bt2",
),
log:
"logs/bowtie2_build/build.log"
params:
extra="" # optional parameters
threads: 8
wrapper:
"0.74.0/bio/bowtie2/build"
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==2.4.1
samtools==1.10
Authors¶
- Daniel Standage
Code¶
__author__ = "Daniel Standage"
__copyright__ = "Copyright 2020, Daniel Standage"
__email__ = "daniel.standage@nbacc.dhs.gov"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
indexbase = snakemake.output[0].replace(".1.bt2", "")
shell(
"bowtie2-build --threads {snakemake.threads} {snakemake.params.extra} "
"{snakemake.input.reference} {indexbase}"
)