Description Usage Arguments Value Author(s) Examples
Creates a summary report from basecalling and demultiplexing metrics.
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object |
A basecall QC object as returned from basecallQC() function |
reportOut |
Name of report file |
reportOutDir |
Directory for the report file |
output |
Whether the report contains frozen or sortable tables. Options are "static" and "html" |
reportRMDfile |
RMD to be used for reporting. (Default uses standard report template) |
FQQC |
TRUE or FALSE, whether to run ShortRead fastq QC on any fastQ in output directory. |
An HTML report is written to file.
Thomas Carroll
1 2 3 4 5 6 7 8 | 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)
outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
reportBCL(bclQC,"TestReport.html",output="html")
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