createBCLcommand {basecallQC} | R Documentation

## Function to create command for Illumina basecalling/demultiplexing using bcl2fastq versions >= 2.1.7.

### 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)

[Package basecallQC version 1.4.0 Index]