protected void |
AbstractIlluminaDemuxDataProcessor.addCommandLineArgument(List<String> args,
RunConfiguration conf,
String longArgName) |
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protected void |
AbstractIlluminaDemuxDataProcessor.addCommandLineArgument(List<String> args,
RunConfiguration conf,
String longArgName,
String defaultValue) |
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protected abstract void |
AbstractIlluminaDemuxDataProcessor.additionalInit(RunConfiguration conf) |
Additional initialization.
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protected void |
Bcl2FastqIlluminaDemuxDataProcessor.additionalInit(RunConfiguration conf) |
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protected void |
BclConvertIlluminaDemuxDataProcessor.additionalInit(RunConfiguration conf) |
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protected abstract List<String> |
AbstractIlluminaDemuxDataProcessor.createDemuxCommandLine(Path inputPath,
Path outputPath,
Path samplesheetPath,
String toolVersion,
RunConfiguration runConf) |
Create the command line to execute the demultiplexing.
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protected List<String> |
Bcl2FastqIlluminaDemuxDataProcessor.createDemuxCommandLine(Path inputPath,
Path outputPath,
Path samplesheetPath,
String bcl2fastqVersion,
RunConfiguration runConf) |
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protected List<String> |
BclConvertIlluminaDemuxDataProcessor.createDemuxCommandLine(Path inputPath,
Path outputPath,
Path samplesheetPath,
String version,
RunConfiguration runConf) |
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DataProcessor.ProcessResult |
AbstractIlluminaDemuxDataProcessor.process(InputData inputData,
RunConfiguration runConf) |
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DataProcessor.ProcessResult |
Aozan2QCDataProcessor.process(InputData inputData,
RunConfiguration runConf) |
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DataProcessor.ProcessResult |
DataProcessor.process(InputData inputData,
RunConfiguration conf) |
Process data.
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DataProcessor.ProcessResult |
DiscoverNewIlluminaRunDataProcessor.process(InputData inputData,
RunConfiguration conf) |
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DataProcessor.ProcessResult |
DoradoONTBasecallingDataProcessor.process(InputData inputData,
RunConfiguration runConf) |
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DataProcessor.ProcessResult |
EndIlluminaRunDataProcessor.process(InputData inputData,
RunConfiguration conf) |
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DataProcessor.ProcessResult |
GuppyONTBasecallingDataProcessor.process(InputData inputData,
RunConfiguration runConf) |
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DataProcessor.ProcessResult |
SyncDataProcessor.process(InputData input,
RunConfiguration runConf) |
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static Settings |
Aozan2Compatibility.runConfigurationToSettings(RunConfiguration runConfiguration) |
Convert an Azoan 3 RunConfiguration object to an Aozan 2 Settings object.
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