fastq2fasta: A function to handle the conversion from fastq to fasta

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

A function to handle the conversion from fastq to fasta

Description

This function executes a ubuntu docker that convert a fastq.gz file in a fasta file using seqtk

Usage

fastq2fasta(group = c("sudo", "docker"), scratch.folder, data.folder)

Arguments

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

Value

Returns sample.fasta file in the data.folder

Author(s)

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

Examples

## Not run: 
    #running fastq2fasta
    fastq2fasta(group="docker", scratch.folder="/data/scratch", data.folder=getwd())

## End(Not run)

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