BWA-MEM2 INDEX

Creates a bwa-mem2 index.

URL:

Example

This wrapper can be used in the following way:

rule bwa_mem2_index:
    input:
        "{genome}",
    output:
        "{genome}.0123",
        "{genome}.amb",
        "{genome}.ann",
        "{genome}.bwt.2bit.64",
        "{genome}.pac",
    log:
        "logs/bwa-mem2_index/{genome}.log",
    params:
        prefix=lambda w: w.genome,
    wrapper:
        "v1.2.1/bio/bwa-mem2/index"

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

• bwa-mem2==2.2.1

Authors

• Christopher Schröder
• Patrik Smeds

Code

__author__ = "Christopher Schröder, Patrik Smeds"
__copyright__ = "Copyright 2020, Christopher Schröder, Patrik Smeds"
__email__ = "christopher.schroeder@tu-dortmund.de, patrik.smeds@gmail.com"
__license__ = "MIT"

from os import path

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

# Check inputs/arguments.
if len(snakemake.input) == 0:
    raise ValueError("A reference genome has to be provided.")
elif len(snakemake.input) > 1:
    raise ValueError("Please provide exactly one reference genome as input.")

# Prefix that should be used for the database
prefix = None
if "prefix" in snakemake.params.keys():
    prefix = snakemake.params["prefix"]
else:
    prefix = splitext(snakemake.output[0])[0]

if len(prefix) > 0:
    prefix = "-p " + prefix

shell("bwa-mem2 index" " {prefix}" " {snakemake.input[0]}" " {log}")