fastq2fasta.Rd
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)
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 |
Returns sample.fasta file in the data.folder
if (FALSE) { #running fastq2fasta fastq2fasta(group="docker", scratch.folder="/data/scratch", data.folder=getwd()) }