TRIMMOMATIC SE¶
Trim single-end reads with trimmomatic.
Software dependencies¶
- trimmomatic ==0.36
Example¶
This wrapper can be used in the following way:
rule trimmomatic_pe:
input:
"reads/{sample}.fastq"
output:
"trimmed/{sample}.fastq.gz"
log:
"logs/trimmomatic/{sample}.log"
params:
# list of trimmers (see manual)
trimmer=["TRAILING:3"],
# optional parameters
extra=""
wrapper:
"0.19.0/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
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 SE {snakemake.params.extra} "
"{snakemake.input} {snakemake.output} "
"{trimmer} "
"{log}")