RAZERS3

Mapping (short) reads against a reference sequence. Can have multiple output formats, please see https://github.com/seqan/seqan/tree/master/apps/razers3

Example

This wrapper can be used in the following way:

rule razers3:
    input:
        # list of input reads
        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"]
    output:
        # output format is automatically inferred from file extension. Can be bam/sam or other formats.
        "mapped/{sample}.bam"
    log:
        "logs/razers3/{sample}.log"
    params:
        # the reference genome
        genome="genome.fasta",
        # additional parameters
        extra=""
    threads: 8
    wrapper:
        "v5.3.0-16-g710597c/bio/razers3"

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

• razers3=3.5.8

Authors

• Jan Forster

Code

__author__ = "Jan Forster"
__copyright__ = "Copyright 2020, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"


import os
from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)


shell(
    "(razers3"
    " -tc {snakemake.threads}"
    " {extra}"
    " -o {snakemake.output[0]}"
    " {snakemake.params.genome}"
    " {snakemake.input.reads})"
    " {log}"
)