A function executing kraken

This function executes a ubuntu docker that embed kraken2

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

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

Examples

if (FALSE) {
    #running skeleton
    kraken(group="docker", scratch.folder="/data/scratch", 
    fastq.folder=getwd(), genome.folder="/data/genomes/minikraken",
    fastq.prefix="unmapped", threads=8)
}