Constant Field Values

Contents

• fr.ens.*

fr.ens.*

fr.ens.biologie.genomique.aozan.Globals

Modifier and Type	Constant Field	Value
public static final String	APP_NAME	"Aozan"
public static final String	EMBEDDED_FASTQSCREEN_PROJECT_XSL	"/fastqscreen_project.xsl"
public static final String	EMBEDDED_FASTQSCREEN_XSL	"/fastqscreen.xsl"
public static final String	EMBEDDED_QC_XSL	"/aozan.xsl"
public static final String	EMBEDDED_UNDETERMINED_XSL	"/undetermined_report.xsl"
public static final String	INDEX_HTML_TEMPLATE_FILENAME	"/template_index_run.html"
public static final String	LICENSE_TXT	"This program is developed under the GNU General Public License version 2 or later and CeCILL-A."
public static final String	QC_DATA_EXTENSION	".data"

fr.ens.biologie.genomique.aozan.QC

Modifier and Type	Constant Field	Value
public static final String	BCL2FASTQ_OUTPUT_DIR	"casava.output.dir"
public static final String	LANE_COUNT	"lane.count"
public static final String	QC_COLLECTOR_NAMES	"qc.collector.names"
public static final String	QC_OUTPUT_DIR	"qc.output.dir"
public static final String	RTA_OUTPUT_DIR	"rta.output.dir"
public static final String	SAMPLESHEET	"samplesheet"
public static final String	TEST_KEY_ENABLED_SUFFIX	".enable"
public static final String	TEST_KEY_PREFIX	"qc.test."
public static final String	TMP_DIR	"tmp.dir"

fr.ens.biologie.genomique.aozan.Settings

Modifier and Type	Constant Field	Value
public static final String	AOZAN_CONF_FILE_PATH	"aozan.configuration.file.path"
public static final String	AOZAN_DEBUG_KEY	"aozan.debug"
public static final String	AOZAN_ENABLE_KEY	"aozan.enable"
public static final String	AOZAN_LOG_LEVEL_KEY	"aozan.log.level"
public static final String	AOZAN_LOG_PATH_KEY	"aozan.log.path"
public static final String	AOZAN_VAR_PATH_KEY	"aozan.var.path"
public static final String	BCL_DATA_PATH_KEY	"bcl.data.path"
public static final String	BCL_SPACE_FACTOR_KEY	"bcl.space.factor"
public static final String	BCL2FASTQ_ADAPTER_FASTA_FILE_PATH_KEY	"bcl2fastq.adapter.fasta.file.path"
public static final String	BCL2FASTQ_ADDITIONNAL_ARGUMENTS_KEY	"bcl2fastq.additionnal.arguments"
public static final String	BCL2FASTQ_COMPRESSION_KEY	"bcl2fastq.compression"
public static final String	BCL2FASTQ_COMPRESSION_LEVEL_KEY	"bcl2fastq.compression.level"
public static final String	BCL2FASTQ_FASTQ_CLUSTER_COUNT_KEY	"bcl2fastq.fastq.cluster.count"
public static final String	BCL2FASTQ_MISMATCHES_KEY	"bcl2fastq.mismatches"
public static final String	BCL2FASTQ_PATH_KEY	"bcl2fastq.path"
public static final String	BCL2FASTQ_USE_DOCKER_KEY	"bcl2fastq.use.docker"
public static final String	BCL2FASTQ_WITH_FAILED_READS_KEY	"bcl2fastq.with.failed.reads"
public static final String	DEMUX_ARCHIVE_SAMPLESHEETS_KEY	"demux.archive.samplesheets"
public static final String	DEMUX_SPACE_FACTOR_KEY	"demux.space.factor"
public static final String	DEMUX_STEP_KEY	"demux.step"
public static final String	DEMUX_THREADS_KEY	"demux.threads"
public static final String	DEMUX_USE_HISEQ_OUTPUT_KEY	"demux.use.hiseq.output"
public static final String	DOCKER_URI_KEY	"docker.uri"
public static final String	FASTQ_DATA_PATH_KEY	"fastq.data.path"
public static final String	FASTQ_SPACE_FACTOR_KEY	"fastq.space.factor"
public static final String	FIRST_BASE_REPORT_STEP_KEY	"first.base.report.step"
public static final String	HISEQ_CRITICAL_MIN_SPACE_KEY	"hiseq.critical.min.space"
public static final String	HISEQ_DATA_PATH_KEY	"hiseq.data.path"
public static final String	HISEQ_SPACE_FACTOR_KEY	"hiseq.space.factor"
public static final String	HISEQ_STEP_KEY	"hiseq.step"
public static final String	HISEQ_WARNING_MIN_SPACE_KEY	"hiseq.warning.min.space"
public static final String	INDEX_HTML_TEMPLATE_KEY	"index.html.template"
public static final String	INDEX_SEQUENCES_KEY	"index.sequences"
public static final String	LOCK_FILE_KEY	"lock.file"
public static final String	MAIL_ERROR_TO_KEY	"mail.error.to"
public static final String	MAIL_FOOTER_KEY	"mail.footer"
public static final String	MAIL_FROM_KEY	"mail.from"
public static final String	MAIL_HEADER_KEY	"mail.header"
public static final String	MAIL_TO_KEY	"mail.to"
public static final String	QC_CONF_FASTQC_ADAPTER_FILE_KEY	"qc.conf.fastqc.adapter.file"
public static final String	QC_CONF_FASTQC_BLAST_ARGUMENTS_KEY	"qc.conf.fastqc.blast.arguments"
public static final String	QC_CONF_FASTQC_BLAST_DB_PATH_KEY	"qc.conf.fastqc.blast.db.path"
public static final String	QC_CONF_FASTQC_BLAST_ENABLE_KEY	"qc.conf.fastqc.blast.enable"
public static final String	QC_CONF_FASTQC_BLAST_PATH_KEY	"qc.conf.fastqc.blast.path"
public static final String	QC_CONF_FASTQC_BLAST_USE_DOCKER_KEY	"qc.conf.fastqc.blast.use.docker"
public static final String	QC_CONF_FASTQC_CASAVA_KEY	"qc.conf.fastqc.casava"
public static final String	QC_CONF_FASTQC_CONTAMINANT_FILE_KEY	"qc.conf.fastqc.contaminant.file"
public static final String	QC_CONF_FASTQC_EXPGROUP_KEY	"qc.conf.fastqc.expgroup"
public static final String	QC_CONF_FASTQC_KEEP_ZIP_REPORT_FILE_KEY	"qc.conf.fastqc.keep.zip.report.file"
public static final String	QC_CONF_FASTQC_KMER_SIZE_KEY	"qc.conf.fastqc.kmer.size"
public static final String	QC_CONF_FASTQC_LIMITS_FILE_KEY	"qc.conf.fastqc.limits.file"
public static final String	QC_CONF_FASTQC_NANO_KEY	"qc.conf.fastqc.nano"
public static final String	QC_CONF_FASTQC_NOFILTER_KEY	"qc.conf.fastqc.nofilter"
public static final String	QC_CONF_FASTQC_NOGROUP_KEY	"qc.conf.fastqc.nogroup"
public static final String	QC_CONF_FASTQC_PROCESS_UNDETERMINED_SAMPLES_KEY	"qc.conf.fastqc.process.undetermined.samples"
public static final String	QC_CONF_FASTQC_UNZIP_REPORT_FILE_KEY	"qc.conf.fastqc.unzip.report.file"
public static final String	QC_CONF_FASTQSCREEN_FASTQ_MAX_READS_PARSED_KEY	"qc.conf.fastqscreen.fastq.max.reads.parsed"
public static final String	QC_CONF_FASTQSCREEN_FASTQ_READS_PF_USED_KEY	"qc.conf.fastqscreen.fastq.reads.pf.used"
public static final String	QC_CONF_FASTQSCREEN_GENOMES_ALIAS_PATH_KEY	"qc.conf.fastqscreen.genome.aliases.path"
public static final String	QC_CONF_FASTQSCREEN_GENOMES_DESC_PATH_KEY	"qc.conf.fastqscreen.genome.descs.path"
public static final String	QC_CONF_FASTQSCREEN_GENOMES_KEY	"qc.conf.fastqscreen.genomes"
public static final String	QC_CONF_FASTQSCREEN_GENOMES_PATH_KEY	"qc.conf.fastqscreen.genomes.path"
public static final String	QC_CONF_FASTQSCREEN_MAPPER_ARGUMENTS_KEY	"qc.conf.fastqscreen.mapper.arguments"
public static final String	QC_CONF_FASTQSCREEN_MAPPER_KEY	"qc.conf.fastqscreen.mapper"
public static final String	QC_CONF_FASTQSCREEN_MAPPERS_INDEXES_PATH_KEY	"qc.conf.fastqscreen.mapper.indexes.path"
public static final String	QC_CONF_FASTQSCREEN_MAPPING_IGNORE_PAIRED_END_MODE_KEY	"qc.conf.fastqscreen.mapping.ignore.paired.end.mode"
public static final String	QC_CONF_FASTQSCREEN_MAPPING_SKIP_CONTROL_LANE_KEY	"qc.conf.fastqscreen.mapping.skip.control.lane"
public static final String	QC_CONF_FASTQSCREEN_MAX_READ_LENGTH_KEY	"qc.conf.fastqscreen.max.read.length"
public static final String	QC_CONF_FASTQSCREEN_PERCENT_PROJECT_CONTAMINATION_THRESHOLD_KEY	"qc.conf.fastqscreen.project.contamination.percent.threshold"
public static final String	QC_CONF_FASTQSCREEN_PROCESS_UNDETERMINED_SAMPLES_KEY	"qc.conf.fastqscreen.process.undetermined.samples"
public static final String	QC_CONF_FASTQSCREEN_PROJECT_XSL_FILE_KEY	"qc.conf.fastqscreen.project.xsl.file"
public static final String	QC_CONF_FASTQSCREEN_XSL_FILE_KEY	"qc.conf.fastqscreen.xsl.file"
public static final String	QC_CONF_MULTIQC_USE_DOCKER_KEY	"qc.conf.multiqc.use.docker"
public static final String	QC_CONF_READ_XML_COLLECTOR_USED_KEY	"qc.conf.read.xml.collector.used"
public static final String	QC_CONF_THREADS_KEY	"qc.conf.threads"
public static final String	QC_CONF_UNDETERMINED_INDEXED_XSL_FILE_KEY	"qc.conf.undetermined.indexed.xsl.file"
public static final String	QC_REPORT_SAVE_RAW_DATA_KEY	"qc.report.save.raw.data"
public static final String	QC_REPORT_SAVE_REPORT_DATA_KEY	"qc.report.save.report.data"
public static final String	QC_REPORT_STYLESHEET_KEY	"qc.report.stylesheet"
public static final String	QC_STEP_KEY	"qc.step"
public static final String	READ_ONLY_OUTPUT_FILES_KEY	"read.only.output.files"
public static final String	RECOMPRESS_COMPRESSION_KEY	"recompress.compression"
public static final String	RECOMPRESS_COMPRESSION_LEVEL_KEY	"recompress.compression.level"
public static final String	RECOMPRESS_DELETE_ORIGINAL_FASTQ_KEY	"recompress.delete.original.fastq.files"
public static final String	RECOMPRESS_STEP_KEY	"recompress.step"
public static final String	RECOMPRESS_THREADS_KEY	"recompress.threads"
public static final String	REPORTS_DATA_PATH_KEY	"reports.data.path"
public static final String	REPORTS_URL_KEY	"reports.url"
public static final String	SAMPLESHEET_FORMAT_KEY	"samplesheet.format"
public static final String	SAMPLESHEET_GENERATOR_COMMAND_KEY	"samplesheet.generator.command"
public static final String	SAMPLESHEET_PATH_KEY	"samplesheet.path"
public static final String	SAMPLESHEET_PREFIX_KEY	"samplesheet.prefix"
public static final String	SEND_MAIL_KEY	"send.mail"
public static final String	SYNC_CONTINUOUS_SYNC_KEY	"sync.continuous.sync"
public static final String	SYNC_CONTINUOUS_SYNC_MIN_AGE_FILES_KEY	"sync.continuous.sync.min.age.files"
public static final String	SYNC_EXCLUDE_CIF_KEY	"sync.exclude.cif"
public static final String	SYNC_SPACE_FACTOR_KEY	"sync.space.factor"
public static final String	SYNC_STEP_KEY	"sync.step"
public static final String	TMP_PATH_KEY	"tmp.path"

fr.ens.biologie.genomique.aozan.aozan3.ConfigurationDefaults

Modifier and Type	Constant Field	Value
public static final String	DOCKER_URI_KEY	"docker.uri"
public static final String	RECIPES_DIRECTORY_KEY	"recipes.path"

fr.ens.biologie.genomique.aozan.aozan3.Globals

Modifier and Type	Constant Field	Value
public static final String	APP_NAME	"Aozan"
public static final String	CONF_FILE_EXTENSION	".conf"
public static final String	LICENSE_TXT	"This program is developed under the GNU General Public License version 2 or later and CeCILL-A."
public static final int	MINIMAL_JAVA_VERSION_REQUIRED	8

fr.ens.biologie.genomique.aozan.aozan3.Main

Modifier and Type	Constant Field	Value
public static final String	APPLICATION_CLASSPATH_JVM_ARG	"application.classpath"
public static final String	APPLICATION_MEMORY	"application.memory"
public static final String	APPLICATION_PATH	"application.path"
public static final String	APPLICATION_SCRIPT	"application.launch.script.path"

fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_MAIL_FOOTER	"\nThe Aozan team.\n"
public static final String	DEFAULT_MAIL_HEADER	"THIS IS AN AUTOMATED MESSAGE.\n"
public static final String	DEFAULT_SUBJECT_PREFIX	"[Aozan] "

fr.ens.biologie.genomique.aozan.aozan3.action.DoradoAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"dorado"

fr.ens.biologie.genomique.aozan.aozan3.action.ExecAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"exec"

fr.ens.biologie.genomique.aozan.aozan3.action.GuppyAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"guppy"

fr.ens.biologie.genomique.aozan.aozan3.action.LegacyAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"legacy"

fr.ens.biologie.genomique.aozan.aozan3.action.ListAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"list"

fr.ens.biologie.genomique.aozan.aozan3.action.SampleSheetConvertAction

Modifier and Type	Constant Field	Value
public static final String	ACTION_NAME	"samplesheetconvert"

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Aozan2QCDataProcessor

Modifier and Type	Constant Field	Value
public static final String	PROCESSOR_NAME	"aozan2qc"

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor

Modifier and Type	Constant Field	Value
public static final String	PROCESSOR_NAME	"illumina_demux"

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor

Modifier and Type	Constant Field	Value
public static final String	BCL_CONVERT_FORBIDDEN_DATA_SECTION	"BCLConvertForbidden_Data"
public static final String	PROCESSOR_NAME	"illumina_bclconvert"

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DiscoverNewIlluminaRunDataProcessor

Modifier and Type	Constant Field	Value
public static final String	PROCESSOR_NAME	"illumina_discover"

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DoradoONTBasecallingDataProcessor

Modifier and Type	Constant Field	Value
public static final String	PROCESSOR_NAME	"dorado_basecaller"

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.EndIlluminaRunDataProcessor

Modifier and Type	Constant Field	Value
public static final String	PROCESSOR_NAME	"illumina_end_run"

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.GuppyONTBasecallingDataProcessor

Modifier and Type	Constant Field	Value
public static final String	PROCESSOR_NAME	"guppy_basecaller"

fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.IlluminaSyncDataProcessor

Modifier and Type	Constant Field	Value
public static final String	PROCESSOR_NAME	"illumina_sync"

fr.ens.biologie.genomique.aozan.aozan3.dataprovider.EmptyRunDataProvider

Modifier and Type	Constant Field	Value
public static final String	PROVIDER_NAME	"empty"

fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaProcessedRunDataProvider

Modifier and Type	Constant Field	Value
public static final String	PROVIDER_NAME	"illumina_fastq"

fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider

Modifier and Type	Constant Field	Value
public static final String	PROVIDER_NAME	"illumina_bcl"

fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.EmptyRunConfigurationProvider

Modifier and Type	Constant Field	Value
public static final String	PROVIDER_NAME	"empty"

fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.IlluminaSamplesheetRunConfigurationProvider

Modifier and Type	Constant Field	Value
public static final String	PROVIDER_NAME	"illumina_samplesheet"

fr.ens.biologie.genomique.aozan.collectors.AozanCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"aozaninfo"
public static final String	PREFIX	"aozan.info"

fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"demux"
public static final String	PREFIX	"demux"

fr.ens.biologie.genomique.aozan.collectors.FastQCCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"fastqc"

fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"fastqscreen"

fr.ens.biologie.genomique.aozan.collectors.GlobalStatsCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"globalstats"

fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"multiqc"
public static final String	MULTIQC_DATA_PREFIX	"multiqc"

fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"primaryanalysismetrics"
public static final String	PREFIX	"primary.analysis.metrics"

fr.ens.biologie.genomique.aozan.collectors.ReadCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"read"
public static final String	READ_DATA_PREFIX	"reads"

fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"runinfo"
public static final String	PREFIX	"run.info"

fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"samplesheet"
public static final String	SAMPLESHEET_DATA_PREFIX	"samplesheet"

fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"subsetfastq"

fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"undeterminedindexes"
public static final String	RUN_DATA_PREFIX	"undeterminedindices"

fr.ens.biologie.genomique.aozan.collectors.interop.ErrorMetricsCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"ErrorMetricsCollector"

fr.ens.biologie.genomique.aozan.collectors.interop.ExtractionMetricsCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"ExtractionMetricsCollector"

fr.ens.biologie.genomique.aozan.collectors.interop.QualityMetricsCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"QualityMetricsCollector"
public static final String	DATA_PREFIX	"qualitymetrics"
public static final String	FORK_VERSION_5	"1.18.64"
public static final String	FORK_VERSION_6	"2.7.1"
public static final String	FORK_VERSION_7	"3.0.0"

fr.ens.biologie.genomique.aozan.collectors.interop.TileMetricsCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"TileMetricsCollector"

fr.ens.biologie.genomique.aozan.collectors.stats.ProjectStatisticsCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"projectstats"
public static final String	COLLECTOR_PREFIX	"projectstats"

fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector

Modifier and Type	Constant Field	Value
public static final String	COLLECTOR_NAME	"pooledsample"
public static final String	COLLECTOR_PREFIX	"pooledsample"
public static final String	UNDETERMINED_SAMPLE	"undetermined"

fr.ens.biologie.genomique.aozan.io.FastqSample

Modifier and Type	Constant Field	Value
public static final String	FASTQ_EXTENSION	".fastq"
public static final String	PROJECT_PREFIX	"Project_"
public static final String	SAMPLE_PREFIX	"Sample_"
public static final String	UNDETERMINED_DIR_NAME	"Undetermined_indices"
public static final String	UNDETERMINED_PREFIX	"Sample_lane"