BOWTIE2_BUILD

Map reads with bowtie2.

Software dependencies

• bowtie2 ==2.4.1
• samtools ==1.10

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:
        "0.67.0/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.

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}"
)