Reaper

Tool for demultiplexing, trimming and filtering sequencing data.

Software dependencies

• reaper >=16.098

Example

rule reaper:
  input:
    "raw/{sample}.fastq" # Path to a (possibly gzipped) fastq file.
  output:
    "trimmed/{sample}.fastq.gz" # Path to the output file.
  params:
    options = "" # Additional command line options.
  wrapper:
    "reaper"

Usage

Run snakemake with

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

to automatically download the wrapper reaper 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

• Jens Preussner