A function to handle the conversion from fastq to fasta

This function executes a ubuntu docker that convert a fastq.gz file in a fasta file using seqtk

fastq2fasta(group = c("sudo", "docker"), scratch.folder, data.folder)

Arguments

group,

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

scratch.folder,

a character string indicating the path of the scratch folder

data.folder,

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

Value

Returns sample.fasta file in the data.folder

Author

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

Examples

if (FALSE) {
    #running fastq2fasta
    fastq2fasta(group="docker", scratch.folder="/data/scratch", data.folder=getwd())
}