TRIMMOMATIC PE

Trim paired-end reads with trimmomatic.

Software dependencies

• trimmomatic ==0.36

Example

This wrapper can be used in the following way:

rule trimmomatic_pe:
    input:
        r1="reads/{sample}.1.fastq",
        r2="reads/{sample}.2.fastq"
    output:
        r1="trimmed/{sample}.1.fastq.gz",
        r2="trimmed/{sample}.2.fastq.gz",
        # reads where trimming entirely removed the mate
        r1_unpaired="trimmed/{sample}.1.unpaired.fastq.gz",
        r2_unpaired="trimmed/{sample}.2.unpaired.fastq.gz"
    log:
        "logs/trimmomatic/{sample}.log"
    params:
        # list of trimmers (see manual)
        trimmer=["TRAILING:3"],
        # optional parameters
        extra=""
    wrapper:
        "0.20.1/bio/trimmomatic/pe"

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

• Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell

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

shell("trimmomatic PE {snakemake.params.extra} "
      "{snakemake.input.r1} {snakemake.input.r2} "
      "{snakemake.output.r1} {snakemake.output.r1_unpaired} "
      "{snakemake.output.r2} {snakemake.output.r2_unpaired} "
      "{trimmer} "
      "{log}")