This function executes the docker container by running CutAdapt algorithm a the input RNA-Seq dataset to remove the sequencing adapters.

cutadapt(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  adapter.type = c("ILLUMINA", "NEB"),
  threads = 1
)

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

data.folder,

a character string indicating where fastq files are located

adapter.type,

a character string. Two options: "ILLUMINA" or "NEB", depending to which miRNA library prep was used: ILLUMINA or NEB

threads,

a number indicating the number of cores to be used from the application

Value

The fastq files of the trimmed sequencing reads

Examples

if (FALSE) { ... }