fastqc: A function to handle a docker containier executing fastqc

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

A function to handle a docker containier executing fastqc

Description

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

Usage

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(s)

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

Examples

## Not run: 
    system("wget http://130.192.119.59/public/test_R1.fastq.gz")
    #running fastqc
    fastqc(group="docker", data.folder=getwd(), large=FALSE)

## End(Not run)

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