demultiplexing: Generating running bcl2fastq

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

Generating running bcl2fastq

Description

This function executes the Illumina bcl2fastq program

Usage

demultiplexing(group = c("sudo", "docker"), data.folder, threads = 8)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
data.folder	a character string indicating the Illumina folder where the Samplesheet.csv is located, and example of Samplesheet.cvs is in inst/examples folder
threads	a number indicating the number of cores to be used from the application

Value

Fastq files

Examples

## Not run: 
    #running rsemstar index for human
    demultiplexing(group="docker",
    data.folder="/home/calogero/Documents/data/lollini/3a_run/170712_NB501050_0097_AH3FGNBGX3",
    threads=24)


## End(Not run)

kendomaniac/docker4seq documentation built on April 8, 2024, 5:39 p.m.