A function to handle a docker containier executing fastqc

This function executes a ubuntu docker that produces as output FASTQCstdin_fastqc.html and stdin_fastqc.zip files

fastqc(group = c("sudo", "docker"), data.folder, large = FALSE)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

data.folder,

a character string indicating the folder where input data are located and where output will be written

large,

boolenan if FALSE uses 10000 reads to make fastq statistics if TRUe uses 1 milion reads

Author

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

Examples

if (FALSE) {
    system("wget http://130.192.119.59/public/test_R1.fastq.gz")
    #running fastqc
    fastqc(group="docker", data.folder=getwd(), large=FALSE)
}