sraDownload: A function to handle fasterq-dumper SRA to download SRA fastq...

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

A function to handle fasterq-dumper SRA to download SRA fastq files

Description

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

Usage

sraDownload(
  group = c("sudo", "docker"),
  sra.name,
  data.folder,
  scratch.folder,
  threads = 8
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
sra.name	a character string indicating the name of the SRA object to be download
data.folder	a character string indicating the working folder where output folder will be written
scratch.folder	a character string indicating the temporary folder for data preprocessing
threads	a integer indicating the number of threads to be used from fasterq-dumper

Author(s)

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

Examples

## Not run: 
    #running sraDownload
    sraDownload(group="docker", sra.name="SRR7762358", data.folder=getwd(), scratch.folder="/data/scratch", threads=8)
    system("mv ./SRR7762358/SRR7762358.fastq.gz ./SRR7762358/SRR7762358_S1_L001_R1_001.fastq.gz")

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.