Cutadapt

Trim single-end or paired-end reads using cutadapt.

Software dependencies

• cutadapt >=1.16

Example

rule cutadapt:
  input:
    "raw/{sample}_R1.fastq.gz", "raw/{sample}_R2.fastq.gz" # Up to two (paired-end) fastq files.
  output:
    fastq1 = "trimmed/{sample}_R1.fastq.gz", # The output file of the first mate.
    fastq2 = "trimmed/{sample}_R2.fastq.gz", # (optional) The output file of the second mate.
    qc = "stats/{sample}.qc" # A text file containing trimming statistics
  params:
    options = "" # Additional command line options.
  wrapper:
    "cutadapt"

Usage

Run snakemake with

snakemake --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/

to automatically download the wrapper cutadapt and include it in the snakefile.

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
• Jens Preussner