CUTADAPT-SE

Trim single-end reads using cutadapt.

Software dependencies

  • cutadapt ==1.13

Example

This wrapper can be used in the following way:

rule cutadapt:
    input:
        "reads/{sample}.fastq"
    output:
        fastq="trimmed/{sample}.fastq",
        qc="trimmed/{sample}.qc.txt"
    params:
        "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 20"
    log:
        "logs/cutadapt/{sample}.log"
    wrapper:
        "0.32.0/bio/cutadapt/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

  • Julian de Ruiter

Code

"""Snakemake wrapper for trimming paired-end reads using cutadapt."""

__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell


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

shell(
    "cutadapt"
    " {snakemake.params}"
    " -o {snakemake.output.fastq}"
    " {snakemake.input[0]}"
    " > {snakemake.output.qc} {log}")