TRIMMOMATIC SE

Trim single-end reads with trimmomatic. (De)compress with pigz.

Software dependencies

  • trimmomatic ==0.36
  • pigz ==2.3.4

Example

This wrapper can be used in the following way:

rule trimmomatic:
    input:
        "reads/{sample}.fastq.gz"  # input and output can be uncompressed or compressed
    output:
        "trimmed/{sample}.fastq.gz"
    log:
        "logs/trimmomatic/{sample}.log"
    params:
        # list of trimmers (see manual)
        trimmer=["TRAILING:3"],
        # optional parameters
        extra="",
        # optional compression levels from -0 to -9 and -11
        compression_level="-9"
    threads:
        32
    wrapper:
        "0.31.0/bio/trimmomatic/se"

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
  • Jorge Langa

Code

"""
bio/trimmomatic/se

Snakemake wrapper to trim reads with trimmomatic in SE mode with help of pigz.
pigz is the parallel implementation of gz. Trimmomatic spends most of the time
compressing and decompressing instead of trimming sequences. By using process
substitution (<(command), >(command)), we can accelerate trimmomatic a lot.
"""

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


from snakemake.shell import shell


def compose_input_gz(filename):
    if filename.endswith(".gz"):
        filename = "<(pigz --decompress --stdout {filename})".format(
            filename=filename
        )
    return filename


def compose_output_gz(filename, compression_level="-5"):
    if filename.endswith(".gz"):
        return ">(pigz {compression_level} > {filename})".format(
            compression_level=compression_level,
            filename=filename
        )
    return filename


extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
compression_level = snakemake.params.get("compression_level", "-5")
trimmer = " ".join(snakemake.params.trimmer)

# Collect files
input = compose_input_gz(snakemake.input[0])
output = compose_output_gz(snakemake.output[0], compression_level)

shell("trimmomatic SE {extra} {input} {output} {trimmer} {log}")