createBCLcommand: Function to create command for Illumina...

In ThomasCarroll/basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files

Description

Creates the command to be used for basecalling/demultiplexing with bcl2fastq versions >= 2.1.7

Usage

createBCLcommand(bcl2fastqparams, cleanedSampleSheet, baseMasks)

Arguments

bcl2fastqparams	A BCL2FastQparams object.
cleanedSampleSheet	Data.frame of cleaned samplesheet for Illumina basecalling/demultiplexing using bcl2fastq versions >= 2.1.7 (see vignette for more details)
baseMasks	A data.frame of basemasks as created by createBasemasks() function

Value

A character vector containing the command for Illumina basecalling using bcl2fastq versions >= 2.1.7

Author(s)

Thomas Carroll and Marian Dore

Examples

fileLocations <- system.file("extdata",package="basecallQC")
runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)

cleanedSampleSheet <- validateBCLSheet(sampleSheet,param=bcl2fastqparams)
baseMasks <- createBasemasks(cleanedSampleSheet,param=bcl2fastqparams)
toSubmit <- createBCLcommand(bcl2fastqparams,cleanedSampleSheet,baseMasks)

ThomasCarroll/basecallQC documentation built on May 9, 2019, 4:45 p.m.