kraken.Rd
This function executes a ubuntu docker that embed kraken2
kraken( group = "docker", scratch.folder, fastq.folder, genome.folder, fastq.prefix, threads )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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 |
if (FALSE) { #running skeleton kraken(group="docker", scratch.folder="/data/scratch", fastq.folder=getwd(), genome.folder="/data/genomes/minikraken", fastq.prefix="unmapped", threads=8) }