kraken: A function executing kraken

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

A function executing kraken

Description

This function executes a ubuntu docker that embed kraken2

Usage

kraken(
  group = "docker",
  scratch.folder,
  fastq.folder,
  genome.folder,
  fastq.prefix,
  threads
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder	a character string indicating the scratch folder where docker container will be mounted
fastq.folder	a character string indicating the folder where input fastq(s) are located and where output will be written
genome.folder	a character string indicating the folder where the indexed kraken db is located
fastq.prefix	a character string indicating the PREFIX of the fastq file(s): e.g. prova_R1.fastq.gz fastq.prefix="prova"
threads	a number indicating the number of cores to be used from the application

Author(s)

Raffaele A Calogero, raffaele.calogero [at] unito [dot] it, University of Torino

Examples

## Not run: 
    #running skeleton
    kraken(group="docker", scratch.folder="/data/scratch", 
    fastq.folder=getwd(), genome.folder="/data/genomes/minikraken",
    fastq.prefix="unmapped", threads=8)

## End(Not run)

kendomaniac/docker4seq documentation built on June 14, 2025, 8:03 a.m.