Index

A

acquire() (auto_process_ngs.utils.FileLock method) activate_env_cmd() (auto_process_ngs.conda.CondaWrapper method) adapter_content_plot() (auto_process_ngs.qc.fastqc.Fastqc method) adapter_content_summary() (auto_process_ngs.qc.fastqc.FastqcData method) add() (auto_process_ngs.barcodes.analysis.BarcodeGroup method) (auto_process_ngs.barcodes.analysis.Reporter method) (auto_process_ngs.docwriter.Para method) (auto_process_ngs.docwriter.Section method) (auto_process_ngs.simple_scheduler.SchedulerGroup method) (auto_process_ngs.utils.ZipArchive method) add_10x_mkfastq_qc_output() (auto_process_ngs.mock.UpdateAnalysisDir method) add_10x_options() (in module auto_process_ngs.cli.run_qc) add_advanced_options() (in module auto_process_ngs.cli.run_qc) add_analyse_barcodes_command() (in module auto_process_ngs.cli.auto_process) add_archive_command() (in module auto_process_ngs.cli.auto_process) add_args() (auto_process_ngs.command.Command method) (auto_process_ngs.pipeliner.PipelineCommandWrapper method) add_barcode_analysis() (auto_process_ngs.mock.UpdateAnalysisDir method) add_block() (auto_process_ngs.pipeliner.PipelineScriptWrapper method) add_call() (auto_process_ngs.pipeliner.PipelineFunctionTask method) add_cellranger_args() (in module auto_process_ngs.tenx.utils) add_cellranger_count() (auto_process_ngs.qc.pipeline.QCPipeline method) add_cellranger_count_outputs() (auto_process_ngs.mock.UpdateAnalysisProject method) add_cellranger_multi_outputs() (auto_process_ngs.mock.UpdateAnalysisProject method) add_cellranger_qc_output() (auto_process_ngs.mock.UpdateAnalysisDir method) add_clone_command() (in module auto_process_ngs.cli.auto_process) add_cmd() (auto_process_ngs.pipeliner.PipelineTask method) add_command() (in module auto_process_ngs.decorators) add_conda_options() (in module auto_process_ngs.cli.run_qc) add_config_command() (in module auto_process_ngs.cli.auto_process) add_css_classes() (auto_process_ngs.docwriter.Para method) (auto_process_ngs.docwriter.Section method) (auto_process_ngs.docwriter.Table method) add_css_rule() (auto_process_ngs.docwriter.Document method) add_debug_options() (in module auto_process_ngs.cli.run_qc) add_deprecated_options() (in module auto_process_ngs.cli.run_qc) add_dir() (auto_process_ngs.utils.ZipArchive method) add_envmodules() (auto_process_ngs.pipeliner.Pipeline method) add_fastq() (auto_process_ngs.analysis.AnalysisSample method) (auto_process_ngs.mock.MockAnalysisProject method) add_fastq_set() (auto_process_ngs.mock.UpdateAnalysisProject method) add_file() (auto_process_ngs.mock.DirectoryUpdater method) (auto_process_ngs.utils.ZipArchive method) add_icell8_outputs() (auto_process_ngs.mock.UpdateAnalysisProject method) add_import_project_command() (in module auto_process_ngs.cli.auto_process) add_info_command() (in module auto_process_ngs.cli.auto_process) add_item() (auto_process_ngs.docwriter.List method) add_javascript() (auto_process_ngs.docwriter.Document method) add_job_control_options() (in module auto_process_ngs.cli.run_qc) add_make_fastqs_command() (in module auto_process_ngs.cli.auto_process) add_merge_fastq_dirs_command() (in module auto_process_ngs.cli.auto_process) add_metadata_command() (in module auto_process_ngs.cli.auto_process) add_metadata_options() (in module auto_process_ngs.cli.run_qc) add_multiplex_analysis_table() (auto_process_ngs.qc.reporting.QCReport method) add_output() (auto_process_ngs.pipeliner.Pipeline method) (auto_process_ngs.pipeliner.PipelineTask method) add_param() (auto_process_ngs.pipeliner.Pipeline method) add_params_command() (in module auto_process_ngs.cli.auto_process) add_per_fastq_statistics() (auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport method) add_per_lane_sample_statistics() (auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport method) add_per_lane_statistics() (auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport method) add_pipeline() (auto_process_ngs.pipeliner.Pipeline method) add_pipeline_options() (in module auto_process_ngs.cli.run_qc) add_processing_report() (auto_process_ngs.mock.UpdateAnalysisDir method) add_project() (auto_process_ngs.metadata.ProjectMetadataFile method) (auto_process_ngs.qc.pipeline.QCPipeline method) add_publish_qc_command() (in module auto_process_ngs.cli.auto_process) add_qc_outputs() (auto_process_ngs.mock.UpdateAnalysisProject method) add_readme_command() (in module auto_process_ngs.cli.auto_process) add_reference_data_options() (in module auto_process_ngs.cli.run_qc) add_report_command() (in module auto_process_ngs.cli.auto_process) add_reporting_options() (in module auto_process_ngs.cli.run_qc) add_row() (auto_process_ngs.docwriter.Table method) add_run_qc_command() (in module auto_process_ngs.cli.auto_process) add_runner() (auto_process_ngs.pipeliner.Pipeline method) add_samplesheet_command() (in module auto_process_ngs.cli.auto_process) add_section() (auto_process_ngs.docwriter.Document method) (auto_process_ngs.settings.Settings method) add_setup_analysis_dirs_command() (in module auto_process_ngs.cli.auto_process) add_setup_command() (in module auto_process_ngs.cli.auto_process) add_single_library_analysis_table() (auto_process_ngs.qc.reporting.QCReport method) add_subdir() (auto_process_ngs.mock.DirectoryUpdater method) add_subsection() (auto_process_ngs.docwriter.Section method) add_summary_table() (auto_process_ngs.qc.reporting.QCReport method) add_task() (auto_process_ngs.pipeliner.Pipeline method) (auto_process_ngs.qc.pipeline.QCPipeline method) add_to_toc() (auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport method) add_update_command() (in module auto_process_ngs.cli.auto_process) add_update_fastq_stats_command() (in module auto_process_ngs.cli.auto_process) analyse() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) analyse_barcodes() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.analyse_barcodes_cmd) AnalyseBarcodes (class in auto_process_ngs.barcodes.pipeline) analysis_dir (auto_process_ngs.analysis.AnalysisDir property) AnalysisDir (class in auto_process_ngs.analysis) AnalysisDirMetadata (class in auto_process_ngs.metadata) AnalysisDirParameters (class in auto_process_ngs.metadata) AnalysisFastq (class in auto_process_ngs.analysis) AnalysisProject (class in auto_process_ngs.analysis) AnalysisProjectInfo (class in auto_process_ngs.metadata) AnalysisProjectQCDirInfo (class in auto_process_ngs.metadata) AnalysisSample (class in auto_process_ngs.analysis) annotated_cells (auto_process_ngs.tenx.metrics.AtacSummary property) announce() (in module auto_process_ngs.cli.run_qc) append_columns() (auto_process_ngs.docwriter.Table method) append_pipeline() (auto_process_ngs.pipeliner.Pipeline method) archive() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.archive_cmd) args (auto_process_ngs.command.Command property) (auto_process_ngs.pipeliner.PipelineTask property) assign_barcodes_single_end() (in module auto_process_ngs.fastq_utils) assign_reads() (in module auto_process_ngs.icell8.atac) associate_task() (auto_process_ngs.pipeliner.BaseParam method) associated_task_id (auto_process_ngs.pipeliner.BaseParam property) atac_median_high_quality_fragments_per_cell (auto_process_ngs.tenx.metrics.MultiomeSummary property) AtacSummary (class in auto_process_ngs.tenx.metrics) auto_process_ngs.analysis module auto_process_ngs.applications module auto_process_ngs.auto_processor module auto_process_ngs.barcodes module auto_process_ngs.barcodes.analysis module auto_process_ngs.barcodes.pipeline module auto_process_ngs.barcodes.splitter module auto_process_ngs.bcl2fastq module auto_process_ngs.bcl2fastq.pipeline module auto_process_ngs.bcl2fastq.reporting module auto_process_ngs.bcl2fastq.utils module auto_process_ngs.cli module auto_process_ngs.cli.auto_process module

auto_process_ngs.cli.build_index module auto_process_ngs.cli.reportqc module auto_process_ngs.cli.run_qc module auto_process_ngs.cli.transfer_data module auto_process_ngs.command module auto_process_ngs.commands module auto_process_ngs.commands.analyse_barcodes_cmd module auto_process_ngs.commands.archive_cmd module auto_process_ngs.commands.clone_cmd module auto_process_ngs.commands.import_project_cmd module auto_process_ngs.commands.make_fastqs_cmd module auto_process_ngs.commands.merge_fastq_dirs_cmd module auto_process_ngs.commands.publish_qc_cmd module auto_process_ngs.commands.report_cmd module auto_process_ngs.commands.run_qc_cmd module auto_process_ngs.commands.samplesheet_cmd module auto_process_ngs.commands.setup_analysis_dirs_cmd module auto_process_ngs.commands.setup_cmd module auto_process_ngs.commands.update_cmd module auto_process_ngs.commands.update_fastq_stats_cmd module auto_process_ngs.conda module auto_process_ngs.config module auto_process_ngs.conftest module auto_process_ngs.css_rules module auto_process_ngs.decorators module auto_process_ngs.docwriter module auto_process_ngs.exceptions module auto_process_ngs.fastq_utils module auto_process_ngs.fileops module auto_process_ngs.icell8 module auto_process_ngs.icell8.atac module auto_process_ngs.icell8.constants module auto_process_ngs.icell8.pipeline module auto_process_ngs.icell8.utils module auto_process_ngs.indexes module auto_process_ngs.metadata module auto_process_ngs.mock module auto_process_ngs.mock10xdata module auto_process_ngs.mockqc module auto_process_ngs.mockqcdata module auto_process_ngs.pipeliner module auto_process_ngs.qc module auto_process_ngs.qc.cellranger module auto_process_ngs.qc.constants module auto_process_ngs.qc.fastq_screen module auto_process_ngs.qc.fastq_stats module auto_process_ngs.qc.fastq_strand module auto_process_ngs.qc.fastqc module auto_process_ngs.qc.outputs module auto_process_ngs.qc.picard module auto_process_ngs.qc.pipeline module auto_process_ngs.qc.plots module auto_process_ngs.qc.protocols module auto_process_ngs.qc.qualimap module auto_process_ngs.qc.reporting module auto_process_ngs.qc.rseqc module auto_process_ngs.qc.seqlens module auto_process_ngs.qc.utils module auto_process_ngs.qc.verification module auto_process_ngs.samplesheet_utils module auto_process_ngs.settings module auto_process_ngs.simple_scheduler module auto_process_ngs.stats module auto_process_ngs.tenx module auto_process_ngs.tenx.cellplex module auto_process_ngs.tenx.metrics module auto_process_ngs.tenx.multiome module auto_process_ngs.tenx.utils module auto_process_ngs.utils module AutoProcess (class in auto_process_ngs.auto_processor) available_bcl2fastq_versions() (in module auto_process_ngs.bcl2fastq.utils)

B

bar() (auto_process_ngs.qc.plots.Plot method) barcode (auto_process_ngs.icell8.utils.ICell8Read1 property) barcode_is_10xgenomics() (in module auto_process_ngs.samplesheet_utils) barcode_is_valid() (in module auto_process_ngs.samplesheet_utils) barcode_lengths() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) barcode_quality (auto_process_ngs.icell8.utils.ICell8Read1 property) BarcodeCounter (class in auto_process_ngs.barcodes.analysis) BarcodeGroup (class in auto_process_ngs.barcodes.analysis) BarcodeMatcher (class in auto_process_ngs.barcodes.splitter) barcodes() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) (auto_process_ngs.barcodes.analysis.SampleSheetBarcodes method) (auto_process_ngs.icell8.utils.ICell8Stats method) (auto_process_ngs.icell8.utils.ICell8WellList method) BaseFastqAttrs (class in auto_process_ngs.fastq_utils) BaseParam (class in auto_process_ngs.pipeliner) bases_mask_is_valid() (in module auto_process_ngs.bcl2fastq.utils)

basic_statistics() (auto_process_ngs.qc.fastqc.FastqcData method) batch_fastqs() (in module auto_process_ngs.icell8.utils) BatchFastqs (class in auto_process_ngs.icell8.pipeline) bbox() (auto_process_ngs.qc.plots.Plot method) bcl2fastq (class in auto_process_ngs.applications) bcl2fastq2() (auto_process_ngs.applications.bcl2fastq static method) (auto_process_ngs.mock.MockAnalysisDirFactory class method) bcl_to_fastq_info() (in module auto_process_ngs.bcl2fastq.utils) bclconvert() (auto_process_ngs.applications.bcl2fastq static method) bclconvert_info() (in module auto_process_ngs.bcl2fastq.utils) block() (auto_process_ngs.qc.plots.Plot method) bowtie() (auto_process_ngs.indexes.IndexBuilder method) bowtie2() (auto_process_ngs.indexes.IndexBuilder method) bowtie2_build_cmd() (in module auto_process_ngs.indexes) bowtie_build_cmd() (in module auto_process_ngs.indexes) BufferedOutputFiles (class in auto_process_ngs.utils) build_fastq_strand_conf() (in module auto_process_ngs.qc.fastq_strand)

C

callback() (auto_process_ngs.simple_scheduler.SimpleScheduler method) canonical_name (auto_process_ngs.analysis.AnalysisFastq property) Capturing (class in auto_process_ngs.pipeliner) casava() (auto_process_ngs.mock.MockAnalysisDirFactory class method) cellranger_arc_count_output() (in module auto_process_ngs.qc.outputs) cellranger_atac_count_output() (in module auto_process_ngs.qc.outputs) cellranger_count() (auto_process_ngs.mockqc.MockQCOutputs class method) cellranger_count_output() (in module auto_process_ngs.qc.outputs) cellranger_exe (auto_process_ngs.qc.cellranger.CellrangerCount property) (auto_process_ngs.qc.cellranger.CellrangerMulti property) cellranger_info() (in module auto_process_ngs.tenx.utils) cellranger_multi() (auto_process_ngs.mockqc.MockQCOutputs class method) cellranger_multi_output() (in module auto_process_ngs.qc.outputs) CellrangerCount (class in auto_process_ngs.qc.cellranger) CellrangerMulti (class in auto_process_ngs.qc.cellranger) CellrangerMultiConfigCsv (class in auto_process_ngs.tenx.cellplex) cells (auto_process_ngs.tenx.metrics.MultiplexSummary property) cells_detected (auto_process_ngs.tenx.metrics.AtacSummary property) check() (auto_process_ngs.utils.ProgressChecker method) check_and_warn() (in module auto_process_ngs.samplesheet_utils) check_barcode_collisions() (in module auto_process_ngs.bcl2fastq.utils) check_cellranger_arc_count_outputs() (in module auto_process_ngs.qc.outputs) check_cellranger_atac_count_outputs() (in module auto_process_ngs.qc.outputs) check_cellranger_count_outputs() (in module auto_process_ngs.qc.outputs) check_conda_env() (in module auto_process_ngs.pipeliner) check_fastq_screen_outputs() (in module auto_process_ngs.qc.outputs) check_fastq_strand_outputs() (in module auto_process_ngs.qc.outputs) check_fastqc_outputs() (in module auto_process_ngs.qc.outputs) check_metadata() (auto_process_ngs.auto_processor.AutoProcess method) CheckCellrangerCountOutputs (class in auto_process_ngs.qc.pipeline) CheckFastQCOutputs (class in auto_process_ngs.qc.pipeline) CheckFastqScreenOutputs (class in auto_process_ngs.qc.pipeline) CheckFastqStrandOutputs (class in auto_process_ngs.qc.pipeline) CheckICell8Barcodes (class in auto_process_ngs.icell8.pipeline) cleanup_atexit() (in module auto_process_ngs.cli.run_qc) (in module auto_process_ngs.simple_scheduler) CleanupDirectory (class in auto_process_ngs.icell8.pipeline) clone() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.clone_cmd) close() (auto_process_ngs.simple_scheduler.SchedulerGroup method) (auto_process_ngs.utils.BufferedOutputFiles method) (auto_process_ngs.utils.OutputFiles method) close_project_names() (auto_process_ngs.samplesheet_utils.SampleSheetLinter method) closed (auto_process_ngs.simple_scheduler.SchedulerGroup property) cmd() (auto_process_ngs.icell8.pipeline.BatchFastqs method) (auto_process_ngs.icell8.pipeline.ConcatFastqs method) (auto_process_ngs.icell8.pipeline.ContaminantFilterFastqPair method) (auto_process_ngs.icell8.pipeline.FilterPolyGReads method) (auto_process_ngs.icell8.pipeline.ICell8Statistics method) (auto_process_ngs.icell8.pipeline.SplitAndFilterFastqPair method) (auto_process_ngs.icell8.pipeline.TrimFastqPair method) (auto_process_ngs.pipeliner.PipelineCommand method) (auto_process_ngs.pipeliner.PipelineCommandWrapper method) (auto_process_ngs.pipeliner.PipelineScriptWrapper method) cmdline (auto_process_ngs.qc.cellranger.CellrangerCount property) (auto_process_ngs.qc.cellranger.CellrangerMulti property) cmdline_file (auto_process_ngs.qc.cellranger.CellrangerCount property) (auto_process_ngs.qc.cellranger.CellrangerMulti property) CollateInsertSizes (class in auto_process_ngs.qc.pipeline) collect_fastq_data() (in module auto_process_ngs.stats) collect_fastq_stats() (auto_process_ngs.icell8.utils.ICell8StatsCollector method) collect_files() (in module auto_process_ngs.pipeliner)

CollectFiles (class in auto_process_ngs.icell8.pipeline) CollectInsertSizeMetrics (class in auto_process_ngs.qc.picard) command (auto_process_ngs.command.Command property) Command (class in auto_process_ngs.command) command_line (auto_process_ngs.command.Command property) comments (auto_process_ngs.qc.reporting.QCProject property) committed_slots (auto_process_ngs.simple_scheduler.SimpleScheduler property) completed (auto_process_ngs.pipeliner.PipelineTask property) (auto_process_ngs.simple_scheduler.SchedulerGroup property) (auto_process_ngs.simple_scheduler.SchedulerJob property) concat_fastqs() (in module auto_process_ngs.icell8.atac) ConcatFastqs (class in auto_process_ngs.icell8.pipeline) conda (auto_process_ngs.conda.CondaWrapper property) conda() (auto_process_ngs.pipeliner.PipelineTask method) conda_dependencies (auto_process_ngs.pipeliner.PipelineTask property) conda_dependency_resolution_completed() (auto_process_ngs.pipeliner.PipelineTask method) conda_env_name (auto_process_ngs.pipeliner.PipelineTask property) CondaCreateEnvError CondaWrapper (class in auto_process_ngs.conda) CondaWrapperError config (auto_process_ngs.qc.cellranger.CellrangerMulti property) Config (class in auto_process_ngs.config) config() (in module auto_process_ngs.cli.auto_process) configureBclToFastq() (auto_process_ngs.applications.bcl2fastq static method) ContaminantFilterFastqPair (class in auto_process_ngs.icell8.pipeline) convert_bases_mask_to_override_cycles() (in module auto_process_ngs.bcl2fastq.utils) convert_to_xlsx() (in module auto_process_ngs.icell8.pipeline) ConvertGTFToBed (class in auto_process_ngs.qc.pipeline) ConvertStatsToXLSX (class in auto_process_ngs.icell8.pipeline) copy() (in module auto_process_ngs.fileops) copy_analysis_project() (in module auto_process_ngs.analysis) copy_command() (in module auto_process_ngs.fileops) copytree() (in module auto_process_ngs.fileops) copytree_command() (in module auto_process_ngs.fileops) count_barcode() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) CountBarcodes (class in auto_process_ngs.barcodes.pipeline) counts (auto_process_ngs.barcodes.analysis.BarcodeGroup property) counts() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) counts_all() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) create() (auto_process_ngs.mock.Mock10xPackageExe static method) (auto_process_ngs.mock.MockAnalysisDir method) (auto_process_ngs.mock.MockAnalysisProject method) (auto_process_ngs.mock.MockBcl2fastq2Exe static method) (auto_process_ngs.mock.MockBclConvertExe static method) (auto_process_ngs.mock.MockBowtie2Build static method) (auto_process_ngs.mock.MockBowtieBuild static method) (auto_process_ngs.mock.MockConda static method) (auto_process_ngs.mock.MockFastQC static method) (auto_process_ngs.mock.MockFastqScreen static method) (auto_process_ngs.mock.MockFastqStrandPy static method) (auto_process_ngs.mock.MockGtf2bed static method) (auto_process_ngs.mock.MockMultiQC static method) (auto_process_ngs.mock.MockPicard static method) (auto_process_ngs.mock.MockQualimap static method) (auto_process_ngs.mock.MockRSeQC static method) (auto_process_ngs.mock.MockSamtools static method) (auto_process_ngs.mock.MockSeqtk static method) (auto_process_ngs.mock.MockStar static method) create_directory() (auto_process_ngs.analysis.AnalysisProject method) create_env() (auto_process_ngs.conda.CondaWrapper method) create_placeholder_fastqs() (in module auto_process_ngs.bcl2fastq.pipeline) css_classes (auto_process_ngs.docwriter.Section property) css_rules (auto_process_ngs.docwriter.Document property)

D

data (auto_process_ngs.qc.fastqc.Fastqc property) (auto_process_ngs.qc.seqlens.SeqLens property) data() (auto_process_ngs.qc.fastqc.FastqcData method) (auto_process_ngs.qc.outputs.QCOutputs method) date_and_time() (in module auto_process_ngs.simple_scheduler) default_log_dir (auto_process_ngs.qc.pipeline.QCPipeline property) default_runner (auto_process_ngs.simple_scheduler.SimpleScheduler property) default_scheduler_reporter() (in module auto_process_ngs.simple_scheduler) default_value() (in module auto_process_ngs.commands.report_cmd) DemultiplexIcell8Atac (class in auto_process_ngs.bcl2fastq.pipeline) detect_barcodes_warnings() (in module auto_process_ngs.barcodes.analysis) detect_processing_qc_warnings() (in module auto_process_ngs.bcl2fastq.reporting) determine_fastq_format() (auto_process_ngs.analysis.AnalysisProject method) determine_paired_end() (auto_process_ngs.analysis.AnalysisProject method) determine_qc_protocol() (in module auto_process_ngs.qc.protocols)

DetermineRequired10xPackage (class in auto_process_ngs.qc.pipeline) dir (auto_process_ngs.qc.cellranger.CellrangerCount property) (auto_process_ngs.qc.cellranger.CellrangerMulti property) (auto_process_ngs.qc.fastqc.Fastqc property) DirectoryUpdater (class in auto_process_ngs.mock) dirn (auto_process_ngs.qc.reporting.QCProject property) disk_usage() (in module auto_process_ngs.fileops) dispatch_function_cmd() (auto_process_ngs.pipeliner.Dispatcher method) Dispatcher (class in auto_process_ngs.pipeliner) display_info() (in module auto_process_ngs.cli.run_qc) dist (auto_process_ngs.qc.seqlens.SeqLens property) dist() (auto_process_ngs.barcodes.splitter.HammingLookup method) distinct_umis() (auto_process_ngs.icell8.utils.ICell8Stats method) Document (class in auto_process_ngs.docwriter) DocumentIcon (class in auto_process_ngs.docwriter) DownloadIcon (class in auto_process_ngs.docwriter)

E

edit_file() (in module auto_process_ngs.utils) edit_readme() (auto_process_ngs.auto_processor.AutoProcess method) edit_samplesheet() (in module auto_process_ngs.commands.samplesheet_cmd) encode_png() (in module auto_process_ngs.qc.plots) encoded_png() (auto_process_ngs.qc.plots.Plot method) env_dir (auto_process_ngs.conda.CondaWrapper property) envmodules (auto_process_ngs.pipeliner.Pipeline property) estimated_number_of_cells (auto_process_ngs.tenx.metrics.AtacSummary property) (auto_process_ngs.tenx.metrics.GexSummary property) (auto_process_ngs.tenx.metrics.MultiomeSummary property)

execute() (auto_process_ngs.pipeliner.Dispatcher method) exists (auto_process_ngs.analysis.AnalysisProject property) exists() (in module auto_process_ngs.fileops) exit_code (auto_process_ngs.pipeliner.PipelineTask property) (auto_process_ngs.simple_scheduler.SchedulerGroup property) (auto_process_ngs.simple_scheduler.SchedulerJob property) ExtraOutputs (class in auto_process_ngs.qc.outputs)

F

fail() (auto_process_ngs.pipeliner.PipelineTask method) failures (auto_process_ngs.qc.fastqc.FastqcSummary property) fastq (auto_process_ngs.qc.seqlens.SeqLens property) fastq_basename() (auto_process_ngs.mockqc.MockQCOutputs class method) fastq_dirs (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv property) fastq_screen_output() (in module auto_process_ngs.qc.outputs) fastq_screen_v0_9_2() (auto_process_ngs.mockqc.MockQCOutputs class method) fastq_statistics() (in module auto_process_ngs.commands.update_fastq_stats_cmd) fastq_strand_output() (in module auto_process_ngs.qc.outputs) fastq_strand_txt (auto_process_ngs.qc.reporting.FastqGroupQCReporter property) fastq_strand_v0_0_4() (auto_process_ngs.mockqc.MockQCOutputs class method) fastq_subset() (auto_process_ngs.analysis.AnalysisSample method) Fastqc (class in auto_process_ngs.qc.fastqc) fastqc_output() (in module auto_process_ngs.qc.outputs) fastqc_summary() (auto_process_ngs.qc.reporting.FastqQCReporter method) fastqc_v0_11_2() (auto_process_ngs.mockqc.MockQCOutputs class method) FastqcData (class in auto_process_ngs.qc.fastqc) FastqcSummary (class in auto_process_ngs.qc.fastqc) FastqGroupQCReporter (class in auto_process_ngs.qc.reporting) fastqiterator() (auto_process_ngs.fastq_utils.FastqReadCounter static method) FastqQCReporter (class in auto_process_ngs.qc.reporting) FastqQualityStats (class in auto_process_ngs.qc.fastq_stats) FastqReadCounter (class in auto_process_ngs.fastq_utils) fastqs (auto_process_ngs.analysis.AnalysisProject property) fastqs_are_symlinks (auto_process_ngs.analysis.AnalysisProject property) (auto_process_ngs.analysis.AnalysisSample property) Fastqscreen (class in auto_process_ngs.qc.fastq_screen) FastqStatistics (class in auto_process_ngs.bcl2fastq.pipeline) (class in auto_process_ngs.stats) FastqStats (class in auto_process_ngs.stats) Fastqstrand (class in auto_process_ngs.qc.fastq_strand) feature_reference_path (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv property) feature_types (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv property) fetch() (auto_process_ngs.tenx.metrics.MetricsSummary method) (auto_process_ngs.tenx.metrics.MultiplexSummary method) fetch_file() (in module auto_process_ngs.utils) fetch_protocol_definition() (in module auto_process_ngs.qc.protocols) fetch_qc_dir() (auto_process_ngs.qc.reporting.QCReport method) fetch_reference_data() (in module auto_process_ngs.settings) fetch_value() (auto_process_ngs.settings.Settings method) (in module auto_process_ngs.commands.report_cmd) FetchPrimaryData (class in auto_process_ngs.bcl2fastq.pipeline) file_name() (auto_process_ngs.utils.OutputFiles method) FileCollector (class in auto_process_ngs.pipeliner) FileLock (class in auto_process_ngs.utils) FileLockError filter_10x_pipelines() (in module auto_process_ngs.qc.verification) filter_barcodes() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) filter_fastqs() (auto_process_ngs.qc.verification.QCVerifier method) (in module auto_process_ngs.qc.verification) FilterContaminatedReads (class in auto_process_ngs.icell8.pipeline) FilterICell8Fastqs (class in auto_process_ngs.icell8.pipeline) FilterPolyGReads (class in auto_process_ngs.icell8.pipeline) final_tasks (auto_process_ngs.pipeliner.Pipeline property) finalise_warnings() (auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport method) find() (auto_process_ngs.simple_scheduler.SimpleScheduler method) find_executables() (in module auto_process_ngs.utils) find_fastqs() (auto_process_ngs.analysis.AnalysisProject method)

finish() (auto_process_ngs.barcodes.pipeline.ReportBarcodeAnalysis method) (auto_process_ngs.bcl2fastq.pipeline.DemultiplexIcell8Atac method) (auto_process_ngs.bcl2fastq.pipeline.FastqStatistics method) (auto_process_ngs.bcl2fastq.pipeline.FetchPrimaryData method) (auto_process_ngs.bcl2fastq.pipeline.Get10xPackage method) (auto_process_ngs.bcl2fastq.pipeline.GetBcl2Fastq method) (auto_process_ngs.bcl2fastq.pipeline.GetBclConvert method) (auto_process_ngs.bcl2fastq.pipeline.MergeFastqDirs method) (auto_process_ngs.bcl2fastq.pipeline.MergeFastqs method) (auto_process_ngs.bcl2fastq.pipeline.ReportProcessingQC method) (auto_process_ngs.bcl2fastq.pipeline.Run10xMkfastq method) (auto_process_ngs.bcl2fastq.pipeline.RunBcl2Fastq method) (auto_process_ngs.bcl2fastq.pipeline.RunBclConvert method) (auto_process_ngs.icell8.pipeline.CheckICell8Barcodes method) (auto_process_ngs.icell8.pipeline.CollectFiles method) (auto_process_ngs.icell8.pipeline.FilterContaminatedReads method) (auto_process_ngs.icell8.pipeline.FilterICell8Fastqs method) (auto_process_ngs.icell8.pipeline.GetICell8PolyGStats method) (auto_process_ngs.icell8.pipeline.GetReadsWithPolyGRegions method) (auto_process_ngs.icell8.pipeline.GroupFastqsByBarcode method) (auto_process_ngs.icell8.pipeline.GroupFastqsBySample method) (auto_process_ngs.icell8.pipeline.MergeBarcodeFastqs method) (auto_process_ngs.icell8.pipeline.MergeSampleFastqs method) (auto_process_ngs.icell8.pipeline.PairFastqs method) (auto_process_ngs.icell8.pipeline.SplitByBarcodes method) (auto_process_ngs.icell8.pipeline.SplitFastqsIntoBatches method) (auto_process_ngs.icell8.pipeline.TrimReads method) (auto_process_ngs.pipeliner.PipelineTask method) (auto_process_ngs.qc.pipeline.CheckCellrangerCountOutputs method) (auto_process_ngs.qc.pipeline.CheckFastQCOutputs method) (auto_process_ngs.qc.pipeline.CheckFastqScreenOutputs method) (auto_process_ngs.qc.pipeline.CheckFastqStrandOutputs method) (auto_process_ngs.qc.pipeline.ConvertGTFToBed method) (auto_process_ngs.qc.pipeline.GetBAMFiles method) (auto_process_ngs.qc.pipeline.GetSeqLengthStats method) (auto_process_ngs.qc.pipeline.RunCellrangerCount method) (auto_process_ngs.qc.pipeline.RunCellrangerMulti method) (auto_process_ngs.qc.pipeline.RunPicardCollectInsertSizeMetrics method) (auto_process_ngs.qc.pipeline.RunQualimapRnaseq method) (auto_process_ngs.qc.pipeline.RunRSeQCGenebodyCoverage method) (auto_process_ngs.qc.pipeline.RunRSeQCInferExperiment method) (auto_process_ngs.qc.pipeline.SetupFastqStrandConf method) (auto_process_ngs.qc.pipeline.SplitFastqsByLane method) (auto_process_ngs.qc.pipeline.VerifyFastqs method) (auto_process_ngs.qc.pipeline.VerifyQC method) finish_task() (auto_process_ngs.pipeliner.PipelineFunctionTask method) (auto_process_ngs.pipeliner.PipelineTask method) flag_warnings() (auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport method) flow_cell_id() (in module auto_process_ngs.tenx.utils) forward (auto_process_ngs.qc.rseqc.InferExperiment property) frac_fragments_overlapping_peaks (auto_process_ngs.tenx.metrics.AtacSummary property) frac_fragments_overlapping_targets (auto_process_ngs.tenx.metrics.AtacSummary property) frac_masked (auto_process_ngs.qc.seqlens.SeqLens property) frac_padded (auto_process_ngs.qc.seqlens.SeqLens property) frac_reads_in_cells (auto_process_ngs.tenx.metrics.GexSummary property) from_fastq() (auto_process_ngs.qc.fastq_stats.FastqQualityStats method) from_fastqc_data() (auto_process_ngs.qc.fastq_stats.FastqQualityStats method) from_specification() (auto_process_ngs.qc.protocols.QCProtocol class method) FunctionParam (class in auto_process_ngs.pipeliner)

G

general (class in auto_process_ngs.applications) genomes (auto_process_ngs.qc.fastq_strand.Fastqstrand property) get() (auto_process_ngs.config.Config method) Get10xPackage (class in auto_process_ngs.bcl2fastq.pipeline) get_10x_value() (auto_process_ngs.qc.reporting.SampleQCReporter method) get_absolute_file_path() (in module auto_process_ngs.commands.update_fastq_stats_cmd) get_analysis_projects() (auto_process_ngs.auto_processor.AutoProcess method) get_analysis_projects_from_dirs() (auto_process_ngs.auto_processor.AutoProcess method) get_bam_basename() (in module auto_process_ngs.qc.utils) get_bases_mask() (in module auto_process_ngs.bcl2fastq.utils) get_bases_mask_10x_atac() (in module auto_process_ngs.tenx.utils) get_bases_mask_10x_multiome() (in module auto_process_ngs.tenx.utils) get_bases_mask_icell8() (in module auto_process_ngs.icell8.utils) get_bases_mask_icell8_atac() (in module auto_process_ngs.icell8.utils) get_batch_size() (in module auto_process_ngs.icell8.utils) get_bcl_converter_config() (auto_process_ngs.settings.Settings method) get_close_names() (in module auto_process_ngs.samplesheet_utils) get_config_dir() (in module auto_process_ngs.settings) get_dependent_tasks() (auto_process_ngs.pipeliner.Pipeline method) get_destination_config() (auto_process_ngs.settings.Settings method) get_exception() (auto_process_ngs.pipeliner.Dispatcher method) get_execution_environment() (in module auto_process_ngs.cli.run_qc) get_fastqs_from_dir() (in module auto_process_ngs.barcodes.splitter) get_install_dir() (in module auto_process_ngs.settings) get_log_subdir() (auto_process_ngs.auto_processor.AutoProcess method) get_nmismatches() (in module auto_process_ngs.bcl2fastq.utils) get_numbered_subdir() (in module auto_process_ngs.utils) get_organism_config() (auto_process_ngs.settings.Settings method) get_organism_list() (in module auto_process_ngs.utils) get_projects() (auto_process_ngs.analysis.AnalysisDir method) get_read_count() (in module auto_process_ngs.fastq_utils) get_read_number() (in module auto_process_ngs.fastq_utils) get_required_samplesheet_format() (in module auto_process_ngs.bcl2fastq.utils) get_result() (auto_process_ngs.pipeliner.Dispatcher method) get_run_config() (in module auto_process_ngs.bcl2fastq.utils) get_sample() (auto_process_ngs.analysis.AnalysisProject method) get_samples() (auto_process_ngs.analysis.AnalysisProject method)

get_seq_data_samples() (in module auto_process_ngs.qc.utils) get_sequence_lengths() (in module auto_process_ngs.qc.seqlens) get_sequencer_config() (auto_process_ngs.settings.Settings method) get_sequencer_platform() (in module auto_process_ngs.bcl2fastq.utils) get_task() (auto_process_ngs.pipeliner.Pipeline method) get_templates_dir() (in module auto_process_ngs.cli.transfer_data) get_value() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) (auto_process_ngs.qc.reporting.SampleQCReporter method) GetBAMFiles (class in auto_process_ngs.qc.pipeline) GetBasesMask10xMultiome (class in auto_process_ngs.bcl2fastq.pipeline) GetBasesMaskIcell8 (class in auto_process_ngs.bcl2fastq.pipeline) GetBasesMaskIcell8Atac (class in auto_process_ngs.bcl2fastq.pipeline) GetBcl2Fastq (class in auto_process_ngs.bcl2fastq.pipeline) GetBclConvert (class in auto_process_ngs.bcl2fastq.pipeline) getboolean() (auto_process_ngs.config.Config method) GetCellrangerMultiConfig (class in auto_process_ngs.qc.pipeline) GetCellrangerReferenceData (class in auto_process_ngs.qc.pipeline) getfloat() (auto_process_ngs.config.Config method) GetICell8PolyGStats (class in auto_process_ngs.icell8.pipeline) GetICell8Stats (class in auto_process_ngs.icell8.pipeline) getint() (auto_process_ngs.config.Config method) GetReadsWithPolyGRegions (class in auto_process_ngs.icell8.pipeline) GetReferenceDataset (class in auto_process_ngs.qc.pipeline) getrunner() (auto_process_ngs.config.Config method) GetSeqLengthStats (class in auto_process_ngs.qc.pipeline) GetSequenceDataFastqs (class in auto_process_ngs.qc.pipeline) GetSequenceDataSamples (class in auto_process_ngs.qc.pipeline) gex_libraries (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv property) gex_library() (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv method) gex_median_genes_per_cell (auto_process_ngs.tenx.metrics.MultiomeSummary property) GexSummary (class in auto_process_ngs.tenx.metrics) group() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) (auto_process_ngs.simple_scheduler.SimpleScheduler method) group_added() (auto_process_ngs.simple_scheduler.SchedulerReporter method) group_end() (auto_process_ngs.simple_scheduler.SchedulerReporter method) group_fastqs_by_name() (in module auto_process_ngs.fastq_utils) GroupFastqsByBarcode (class in auto_process_ngs.icell8.pipeline) GroupFastqsBySample (class in auto_process_ngs.icell8.pipeline)

H

hamming_distance() (auto_process_ngs.barcodes.splitter.HammingMetrics class method) hamming_distance_truncate() (auto_process_ngs.barcodes.splitter.HammingMetrics class method) hamming_distance_with_N() (auto_process_ngs.barcodes.splitter.HammingMetrics class method) HammingLookup (class in auto_process_ngs.barcodes.splitter) HammingMetrics (class in auto_process_ngs.barcodes.splitter) has_10x_indices() (in module auto_process_ngs.tenx.utils) has_chromium_sc_indices() (in module auto_process_ngs.tenx.utils) has_exe (auto_process_ngs.command.Command property) has_invalid_barcodes() (auto_process_ngs.samplesheet_utils.SampleSheetLinter method) has_invalid_characters() (auto_process_ngs.samplesheet_utils.SampleSheetLinter method) (in module auto_process_ngs.samplesheet_utils) has_invalid_lines() (auto_process_ngs.samplesheet_utils.SampleSheetLinter method) has_lock (auto_process_ngs.utils.FileLock property) has_name() (auto_process_ngs.simple_scheduler.SimpleScheduler method) has_parameter_file (auto_process_ngs.auto_processor.AutoProcess property) has_subsections() (auto_process_ngs.settings.Settings method)

has_warnings (auto_process_ngs.barcodes.analysis.Reporter property) histogram (auto_process_ngs.qc.picard.CollectInsertSizeMetrics property) hline() (auto_process_ngs.qc.plots.Plot method) href (auto_process_ngs.docwriter.Link property) html() (auto_process_ngs.docwriter.Document method) (auto_process_ngs.docwriter.Img method) (auto_process_ngs.docwriter.Link method) (auto_process_ngs.docwriter.List method) (auto_process_ngs.docwriter.Para method) (auto_process_ngs.docwriter.Section method) (auto_process_ngs.docwriter.Table method) (auto_process_ngs.docwriter.Target method) (auto_process_ngs.qc.reporting.ToggleButton method) html_report (auto_process_ngs.qc.fastqc.Fastqc property) (auto_process_ngs.qc.qualimap.QualimapRnaseq property) html_report() (auto_process_ngs.qc.fastqc.FastqcSummary method) html_table() (auto_process_ngs.qc.fastqc.FastqcSummary method)

I

ICell8FastqIterator (class in auto_process_ngs.icell8.utils) ICell8FinalReporting (class in auto_process_ngs.icell8.pipeline) ICell8QCFilter (class in auto_process_ngs.icell8.pipeline) ICell8Read1 (class in auto_process_ngs.icell8.utils) ICell8ReadPair (class in auto_process_ngs.icell8.utils) ICell8Statistics (class in auto_process_ngs.icell8.pipeline) ICell8Stats (class in auto_process_ngs.icell8.utils) ICell8StatsCollector (class in auto_process_ngs.icell8.utils) ICell8WellList (class in auto_process_ngs.icell8.utils) id (auto_process_ngs.qc.reporting.QCProject property) id() (auto_process_ngs.pipeliner.PipelineTask method) identify_seq_data() (auto_process_ngs.qc.verification.QCVerifier method) IdentifyPlatform (class in auto_process_ngs.bcl2fastq.pipeline) IlluminaFastqAttrs (class in auto_process_ngs.fastq_utils) Img (class in auto_process_ngs.docwriter) import_project() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.import_project_cmd) import_samplesheet() (in module auto_process_ngs.commands.samplesheet_cmd) in_error_state (auto_process_ngs.simple_scheduler.SchedulerJob property) IndexBuilder (class in auto_process_ngs.indexes) infer_experiment() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) InferExperiment (class in auto_process_ngs.qc.rseqc) info() (in module auto_process_ngs.cli.auto_process) InfoAction (class in auto_process_ngs.cli.run_qc) init() (auto_process_ngs.barcodes.pipeline.CountBarcodes method) (auto_process_ngs.barcodes.pipeline.ListBarcodeCountFiles method) (auto_process_ngs.barcodes.pipeline.LoadIlluminaData method) (auto_process_ngs.barcodes.pipeline.ReportBarcodeAnalysis method) (auto_process_ngs.barcodes.pipeline.SetupBarcodeAnalysisDirs method) (auto_process_ngs.bcl2fastq.pipeline.DemultiplexIcell8Atac method) (auto_process_ngs.bcl2fastq.pipeline.FastqStatistics method) (auto_process_ngs.bcl2fastq.pipeline.FetchPrimaryData method) (auto_process_ngs.bcl2fastq.pipeline.Get10xPackage method) (auto_process_ngs.bcl2fastq.pipeline.GetBasesMask10xMultiome method) (auto_process_ngs.bcl2fastq.pipeline.GetBasesMaskIcell8 method) (auto_process_ngs.bcl2fastq.pipeline.GetBasesMaskIcell8Atac method) (auto_process_ngs.bcl2fastq.pipeline.GetBcl2Fastq method) (auto_process_ngs.bcl2fastq.pipeline.GetBclConvert method) (auto_process_ngs.bcl2fastq.pipeline.IdentifyPlatform method) (auto_process_ngs.bcl2fastq.pipeline.MakeSampleSheet method) (auto_process_ngs.bcl2fastq.pipeline.MergeFastqDirs method) (auto_process_ngs.bcl2fastq.pipeline.MergeFastqs method) (auto_process_ngs.bcl2fastq.pipeline.ReportProcessingQC method) (auto_process_ngs.bcl2fastq.pipeline.RestoreBackupDirectory method) (auto_process_ngs.bcl2fastq.pipeline.Run10xMkfastq method) (auto_process_ngs.bcl2fastq.pipeline.RunBcl2Fastq method) (auto_process_ngs.bcl2fastq.pipeline.RunBclConvert method) (auto_process_ngs.icell8.pipeline.BatchFastqs method) (auto_process_ngs.icell8.pipeline.CheckICell8Barcodes method) (auto_process_ngs.icell8.pipeline.CleanupDirectory method) (auto_process_ngs.icell8.pipeline.CollectFiles method) (auto_process_ngs.icell8.pipeline.ConcatFastqs method) (auto_process_ngs.icell8.pipeline.ContaminantFilterFastqPair method) (auto_process_ngs.icell8.pipeline.ConvertStatsToXLSX method) (auto_process_ngs.icell8.pipeline.FilterContaminatedReads method) (auto_process_ngs.icell8.pipeline.FilterICell8Fastqs method) (auto_process_ngs.icell8.pipeline.FilterPolyGReads method) (auto_process_ngs.icell8.pipeline.GetICell8Stats method) (auto_process_ngs.icell8.pipeline.GetReadsWithPolyGRegions method) (auto_process_ngs.icell8.pipeline.GroupFastqsByBarcode method) (auto_process_ngs.icell8.pipeline.GroupFastqsBySample method) (auto_process_ngs.icell8.pipeline.ICell8Statistics method) (auto_process_ngs.icell8.pipeline.MergeBarcodeFastqs method) (auto_process_ngs.icell8.pipeline.MergeSampleFastqs method) (auto_process_ngs.icell8.pipeline.PairFastqs method) (auto_process_ngs.icell8.pipeline.ReportProcessing method) (auto_process_ngs.icell8.pipeline.SetupDirectories method) (auto_process_ngs.icell8.pipeline.SplitAndFilterFastqPair method) (auto_process_ngs.icell8.pipeline.SplitByBarcodes method) (auto_process_ngs.icell8.pipeline.SplitFastqsIntoBatches method) (auto_process_ngs.icell8.pipeline.TrimFastqPair method) (auto_process_ngs.icell8.pipeline.TrimReads method) (auto_process_ngs.icell8.pipeline.UpdateProjectData method) (auto_process_ngs.pipeliner.PipelineCommand method) (auto_process_ngs.pipeliner.PipelineCommandWrapper method) (auto_process_ngs.pipeliner.PipelineScriptWrapper method) (auto_process_ngs.pipeliner.PipelineTask method) (auto_process_ngs.qc.pipeline.CheckCellrangerCountOutputs method) (auto_process_ngs.qc.pipeline.CheckFastQCOutputs method) (auto_process_ngs.qc.pipeline.CheckFastqScreenOutputs method) (auto_process_ngs.qc.pipeline.CheckFastqStrandOutputs method) (auto_process_ngs.qc.pipeline.CollateInsertSizes method) (auto_process_ngs.qc.pipeline.ConvertGTFToBed method) (auto_process_ngs.qc.pipeline.DetermineRequired10xPackage method) (auto_process_ngs.qc.pipeline.GetBAMFiles method) (auto_process_ngs.qc.pipeline.GetCellrangerMultiConfig method) (auto_process_ngs.qc.pipeline.GetCellrangerReferenceData method) (auto_process_ngs.qc.pipeline.GetReferenceDataset method) (auto_process_ngs.qc.pipeline.GetSeqLengthStats method) (auto_process_ngs.qc.pipeline.GetSequenceDataFastqs method) (auto_process_ngs.qc.pipeline.GetSequenceDataSamples method) (auto_process_ngs.qc.pipeline.MakeCellrangerArcCountLibraries method) (auto_process_ngs.qc.pipeline.ReportQC method) (auto_process_ngs.qc.pipeline.RunCellrangerCount method) (auto_process_ngs.qc.pipeline.RunCellrangerMulti method) (auto_process_ngs.qc.pipeline.RunFastQC method) (auto_process_ngs.qc.pipeline.RunFastqScreen method) (auto_process_ngs.qc.pipeline.RunFastqStrand method) (auto_process_ngs.qc.pipeline.RunPicardCollectInsertSizeMetrics method) (auto_process_ngs.qc.pipeline.RunQualimapRnaseq method) (auto_process_ngs.qc.pipeline.RunRSeQCGenebodyCoverage method) (auto_process_ngs.qc.pipeline.RunRSeQCInferExperiment method) (auto_process_ngs.qc.pipeline.SetCellCountFromCellranger method) (auto_process_ngs.qc.pipeline.SetupFastqStrandConf method) (auto_process_ngs.qc.pipeline.SetupQCDirs method) (auto_process_ngs.qc.pipeline.SplitFastqsByLane method) (auto_process_ngs.qc.pipeline.UpdateQCMetadata method) (auto_process_ngs.qc.pipeline.VerifyFastqs method) (auto_process_ngs.qc.pipeline.VerifyQC method)

init_readme() (auto_process_ngs.auto_processor.AutoProcess method) init_toc() (auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport method) init_warnings() (auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport method) initial_tasks (auto_process_ngs.pipeliner.Pipeline property) input (auto_process_ngs.qc.qualimap.QualimapRnaseq property) insert_size_metrics() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) install() (auto_process_ngs.conda.CondaWrapper method) invoke() (auto_process_ngs.pipeliner.PipelineTask method) (auto_process_ngs.simple_scheduler.SchedulerCallback method) is_analysis_dir (auto_process_ngs.analysis.AnalysisProject property) is_empty() (auto_process_ngs.simple_scheduler.SimpleScheduler method) is_installed (auto_process_ngs.conda.CondaWrapper property) is_remote (auto_process_ngs.utils.Location property) is_running (auto_process_ngs.simple_scheduler.SchedulerGroup property) (auto_process_ngs.simple_scheduler.SchedulerJob property) is_single_cell (auto_process_ngs.qc.reporting.QCProject property) is_url (auto_process_ngs.utils.Location property) isdir() (in module auto_process_ngs.fileops)

J

job_end() (auto_process_ngs.simple_scheduler.SchedulerReporter method) job_number (auto_process_ngs.simple_scheduler.SimpleScheduler property)

job_scheduled() (auto_process_ngs.simple_scheduler.SchedulerReporter method) job_start() (auto_process_ngs.simple_scheduler.SchedulerReporter method) jobs (auto_process_ngs.simple_scheduler.SchedulerGroup property)

K

keys_in_file() (auto_process_ngs.metadata.MetadataDict method)

L

lane_names (auto_process_ngs.stats.FastqStatistics property) lanes (auto_process_ngs.barcodes.analysis.BarcodeCounter property) (auto_process_ngs.stats.FastqStats property) level (auto_process_ngs.docwriter.Section property) libraries (auto_process_ngs.qc.fastq_screen.Fastqscreen property) libraries() (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv method) library() (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv method) Link (class in auto_process_ngs.docwriter) link_to_module() (auto_process_ngs.qc.fastqc.FastqcSummary method) link_to_output() (auto_process_ngs.qc.qualimap.QualimapRnaseq method) linked_projects() (auto_process_ngs.tenx.multiome.MultiomeLibraries method) linked_samples() (auto_process_ngs.tenx.multiome.MultiomeLibraries method) LinkIcon (class in auto_process_ngs.docwriter) List (class in auto_process_ngs.docwriter) list_envs (auto_process_ngs.conda.CondaWrapper property) list_params() (auto_process_ngs.settings.Settings method) ListBarcodeCountFiles (class in auto_process_ngs.barcodes.pipeline) listdir() (in module auto_process_ngs.fileops)

ListParam (class in auto_process_ngs.pipeliner) load() (auto_process_ngs.metadata.MetadataDict method) load_metadata() (auto_process_ngs.auto_processor.AutoProcess method) load_parameters() (auto_process_ngs.auto_processor.AutoProcess method) load_project_metadata() (auto_process_ngs.auto_processor.AutoProcess method) LoadIlluminaData (class in auto_process_ngs.barcodes.pipeline) local_samples (auto_process_ngs.tenx.multiome.MultiomeLibraries property) locate_project() (in module auto_process_ngs.analysis) locate_project_info_file() (in module auto_process_ngs.analysis) locate_run() (in module auto_process_ngs.analysis) locate_settings_file() (in module auto_process_ngs.settings) Location (class in auto_process_ngs.utils) log_file (auto_process_ngs.qc.rseqc.InferExperiment property) logger (in module auto_process_ngs.qc.fastq_strand) (in module auto_process_ngs.qc.fastqc) lookup() (auto_process_ngs.metadata.ProjectMetadataFile method) (auto_process_ngs.simple_scheduler.SimpleScheduler method) lookup_barcode() (auto_process_ngs.barcodes.analysis.SampleSheetBarcodes method) lookup_sample() (auto_process_ngs.barcodes.analysis.SampleSheetBarcodes method)

M

main() (auto_process_ngs.mock.Mock10xPackageExe method) (auto_process_ngs.mock.MockBcl2fastq2Exe method) (auto_process_ngs.mock.MockBclConvertExe method) (auto_process_ngs.mock.MockBowtie2Build method) (auto_process_ngs.mock.MockBowtieBuild method) (auto_process_ngs.mock.MockFastQC method) (auto_process_ngs.mock.MockFastqScreen method) (auto_process_ngs.mock.MockFastqStrandPy method) (auto_process_ngs.mock.MockGtf2bed method) (auto_process_ngs.mock.MockMultiQC method) (auto_process_ngs.mock.MockPicard method) (auto_process_ngs.mock.MockQualimap method) (auto_process_ngs.mock.MockRSeQC method) (auto_process_ngs.mock.MockSamtools method) (auto_process_ngs.mock.MockSeqtk method) (auto_process_ngs.mock.MockStar method) (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.cli.transfer_data) make() (auto_process_ngs.applications.general static method) make_conda_env() (in module auto_process_ngs.pipeliner) make_conda_env_name() (in module auto_process_ngs.conda) make_custom_sample_sheet() (in module auto_process_ngs.bcl2fastq.utils) make_fastqs() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.make_fastqs_cmd) make_mock_analysis_project() (in module auto_process_ngs.mock) make_mock_bcl2fastq2_output() (in module auto_process_ngs.mock) make_mock_qc_dir() (in module auto_process_ngs.mockqc) make_multi_config_template() (in module auto_process_ngs.tenx.utils) make_plot() (in module auto_process_ngs.qc.plots) make_project_metadata_file() (auto_process_ngs.auto_processor.AutoProcess method) make_qc_summary_html() (in module auto_process_ngs.tenx.utils) make_title() (in module auto_process_ngs.barcodes.analysis) make_wrapper_script() (auto_process_ngs.command.Command method) (auto_process_ngs.pipeliner.PipelineCommand method) MakeCellrangerArcCountLibraries (class in auto_process_ngs.qc.pipeline) MakeFastqs (class in auto_process_ngs.bcl2fastq.pipeline) MakeSampleSheet (class in auto_process_ngs.bcl2fastq.pipeline) masked_dist (auto_process_ngs.qc.seqlens.SeqLens property) match() (auto_process_ngs.barcodes.analysis.BarcodeGroup method) (auto_process_ngs.barcodes.splitter.BarcodeMatcher method) match_run_id() (in module auto_process_ngs.analysis) max_length (auto_process_ngs.qc.seqlens.SeqLens property) mean (auto_process_ngs.qc.seqlens.SeqLens property) mean_reads_per_cell (auto_process_ngs.tenx.metrics.GexSummary property) (auto_process_ngs.tenx.metrics.MultiplexSummary property) median_fragments_per_cell (auto_process_ngs.tenx.metrics.AtacSummary property) median_genes_per_cell (auto_process_ngs.tenx.metrics.GexSummary property) (auto_process_ngs.tenx.metrics.MultiplexSummary property) median_reads_per_cell (auto_process_ngs.tenx.metrics.MultiplexSummary property) median_umi_counts_per_cell (auto_process_ngs.tenx.metrics.MultiplexSummary property) merge_fastq_dirs() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.merge_fastq_dirs_cmd) merge_pipeline() (auto_process_ngs.pipeliner.Pipeline method) MergeBarcodeFastqs (class in auto_process_ngs.icell8.pipeline) MergeFastqDirs (class in auto_process_ngs.bcl2fastq.pipeline) MergeFastqs (class in auto_process_ngs.bcl2fastq.pipeline) MergeSampleFastqs (class in auto_process_ngs.icell8.pipeline) metadata() (in module auto_process_ngs.cli.auto_process) metadata_file (auto_process_ngs.auto_processor.AutoProcess property) MetadataDict (class in auto_process_ngs.metadata) metrics (auto_process_ngs.qc.cellranger.CellrangerCount property) (auto_process_ngs.qc.picard.CollectInsertSizeMetrics property) metrics() (auto_process_ngs.qc.cellranger.CellrangerMulti method) metrics_csv (auto_process_ngs.qc.cellranger.CellrangerCount property) metrics_csv() (auto_process_ngs.qc.cellranger.CellrangerMulti method) metrics_file (auto_process_ngs.qc.picard.CollectInsertSizeMetrics property) MetricsSummary (class in auto_process_ngs.tenx.metrics) min_barcode_quality (auto_process_ngs.icell8.utils.ICell8Read1 property) min_length (auto_process_ngs.qc.seqlens.SeqLens property) min_umi_quality (auto_process_ngs.icell8.utils.ICell8Read1 property) MissingMetricError MissingParameterFileException mkdir() (in module auto_process_ngs.fileops) Mock10xPackageExe (class in auto_process_ngs.mock) MockAnalysisDir (class in auto_process_ngs.mock) MockAnalysisDirFactory (class in auto_process_ngs.mock) MockAnalysisProject (class in auto_process_ngs.mock) MockBcl2fastq2Exe (class in auto_process_ngs.mock) MockBclConvertExe (class in auto_process_ngs.mock) MockBowtie2Build (class in auto_process_ngs.mock) MockBowtieBuild (class in auto_process_ngs.mock) MockCellrangerExe (class in auto_process_ngs.mock) MockConda (class in auto_process_ngs.mock) MockFastQC (class in auto_process_ngs.mock) MockFastqScreen (class in auto_process_ngs.mock) MockFastqStrandPy (class in auto_process_ngs.mock) MockGtf2bed (class in auto_process_ngs.mock) MockMultiQC (class in auto_process_ngs.mock) MockPicard (class in auto_process_ngs.mock) MockQCOutputs (class in auto_process_ngs.mockqc) MockQualimap (class in auto_process_ngs.mock) MockRSeQC (class in auto_process_ngs.mock)

MockSamtools (class in auto_process_ngs.mock) MockSeqtk (class in auto_process_ngs.mock) MockStar (class in auto_process_ngs.mock) module auto_process_ngs.analysis auto_process_ngs.applications auto_process_ngs.auto_processor auto_process_ngs.barcodes auto_process_ngs.barcodes.analysis auto_process_ngs.barcodes.pipeline auto_process_ngs.barcodes.splitter auto_process_ngs.bcl2fastq auto_process_ngs.bcl2fastq.pipeline auto_process_ngs.bcl2fastq.reporting auto_process_ngs.bcl2fastq.utils auto_process_ngs.cli auto_process_ngs.cli.auto_process auto_process_ngs.cli.build_index auto_process_ngs.cli.reportqc auto_process_ngs.cli.run_qc auto_process_ngs.cli.transfer_data auto_process_ngs.command auto_process_ngs.commands auto_process_ngs.commands.analyse_barcodes_cmd auto_process_ngs.commands.archive_cmd auto_process_ngs.commands.clone_cmd auto_process_ngs.commands.import_project_cmd auto_process_ngs.commands.make_fastqs_cmd auto_process_ngs.commands.merge_fastq_dirs_cmd auto_process_ngs.commands.publish_qc_cmd auto_process_ngs.commands.report_cmd auto_process_ngs.commands.run_qc_cmd auto_process_ngs.commands.samplesheet_cmd auto_process_ngs.commands.setup_analysis_dirs_cmd auto_process_ngs.commands.setup_cmd auto_process_ngs.commands.update_cmd auto_process_ngs.commands.update_fastq_stats_cmd auto_process_ngs.conda auto_process_ngs.config auto_process_ngs.conftest auto_process_ngs.css_rules auto_process_ngs.decorators auto_process_ngs.docwriter auto_process_ngs.exceptions auto_process_ngs.fastq_utils auto_process_ngs.fileops auto_process_ngs.icell8 auto_process_ngs.icell8.atac auto_process_ngs.icell8.constants auto_process_ngs.icell8.pipeline auto_process_ngs.icell8.utils auto_process_ngs.indexes auto_process_ngs.metadata auto_process_ngs.mock auto_process_ngs.mock10xdata auto_process_ngs.mockqc auto_process_ngs.mockqcdata auto_process_ngs.pipeliner auto_process_ngs.qc auto_process_ngs.qc.cellranger auto_process_ngs.qc.constants auto_process_ngs.qc.fastq_screen auto_process_ngs.qc.fastq_stats auto_process_ngs.qc.fastq_strand auto_process_ngs.qc.fastqc auto_process_ngs.qc.outputs auto_process_ngs.qc.picard auto_process_ngs.qc.pipeline auto_process_ngs.qc.plots auto_process_ngs.qc.protocols auto_process_ngs.qc.qualimap auto_process_ngs.qc.reporting auto_process_ngs.qc.rseqc auto_process_ngs.qc.seqlens auto_process_ngs.qc.utils auto_process_ngs.qc.verification auto_process_ngs.samplesheet_utils auto_process_ngs.settings auto_process_ngs.simple_scheduler auto_process_ngs.stats auto_process_ngs.tenx auto_process_ngs.tenx.cellplex auto_process_ngs.tenx.metrics auto_process_ngs.tenx.multiome auto_process_ngs.tenx.utils auto_process_ngs.utils modules (auto_process_ngs.qc.fastqc.FastqcData property) MultiomeLibraries (class in auto_process_ngs.tenx.multiome) MultiomeSummary (class in auto_process_ngs.tenx.metrics) multiple_fastqs (auto_process_ngs.analysis.AnalysisProject property) MultiplexSummary (class in auto_process_ngs.tenx.metrics) multiqc() (auto_process_ngs.mockqc.MockQCOutputs class method)

N

n_finished (auto_process_ngs.simple_scheduler.SimpleScheduler property) n_projects (auto_process_ngs.analysis.AnalysisDir property) n_running (auto_process_ngs.simple_scheduler.SimpleScheduler property) n_sequencing_data (auto_process_ngs.analysis.AnalysisDir property) n_waiting (auto_process_ngs.simple_scheduler.SimpleScheduler property) name (auto_process_ngs.docwriter.Img property) (auto_process_ngs.docwriter.Section property) (auto_process_ngs.docwriter.Target property) (auto_process_ngs.pipeliner.Pipeline property) (auto_process_ngs.pipeliner.PipelineParam property) (auto_process_ngs.qc.reporting.QCProject property) (auto_process_ngs.stats.FastqStats property) name() (auto_process_ngs.pipeliner.PipelineCommand method) (auto_process_ngs.pipeliner.PipelineTask method)

nbases (auto_process_ngs.qc.fastq_stats.FastqQualityStats property) njobs() (auto_process_ngs.pipeliner.PipelineTask method) nmasked (auto_process_ngs.qc.seqlens.SeqLens property) no_header() (auto_process_ngs.docwriter.Table method) no_hits (auto_process_ngs.qc.fastq_screen.Fastqscreen property) normalise_data() (auto_process_ngs.qc.plots.Plot method) normalise_organism_name() (in module auto_process_ngs.utils) normalize_sample_name() (in module auto_process_ngs.icell8.utils) npadded (auto_process_ngs.qc.seqlens.SeqLens property) nreads (auto_process_ngs.qc.seqlens.SeqLens property) nreads() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) (auto_process_ngs.icell8.utils.ICell8Stats method) nrows (auto_process_ngs.docwriter.Table property) null_items() (auto_process_ngs.metadata.MetadataDict method) NullValue (class in auto_process_ngs.config)

O

open() (auto_process_ngs.utils.BufferedOutputFiles method) (auto_process_ngs.utils.OutputFiles method)

output (auto_process_ngs.pipeliner.Pipeline property) (auto_process_ngs.pipeliner.PipelineTask property) OutputFiles (class in auto_process_ngs.utils)

P

paginate() (in module auto_process_ngs.utils) pair_fastqs() (in module auto_process_ngs.fastq_utils) pair_fastqs_by_name() (in module auto_process_ngs.fastq_utils) paired_end (auto_process_ngs.analysis.AnalysisDir property) (auto_process_ngs.auto_processor.AutoProcess property) (auto_process_ngs.qc.reporting.FastqGroupQCReporter property) (auto_process_ngs.qc.rseqc.InferExperiment property) PairFastqs (class in auto_process_ngs.icell8.pipeline) Para (class in auto_process_ngs.docwriter) parameter_file (auto_process_ngs.auto_processor.AutoProcess property) params (auto_process_ngs.pipeliner.Pipeline property) params() (in module auto_process_ngs.cli.auto_process) parse_protocol_spec() (in module auto_process_ngs.qc.protocols) parse_qc_module_spec() (in module auto_process_ngs.qc.verification) parse_samplesheet_spec() (in module auto_process_ngs.utils) parse_version() (in module auto_process_ngs.utils) pass_quality_filter() (in module auto_process_ngs.icell8.utils) passes (auto_process_ngs.qc.fastqc.FastqcSummary property) path (auto_process_ngs.qc.fastqc.FastqcData property) (auto_process_ngs.utils.Location property) PathExistsParam (class in auto_process_ngs.pipeliner) PathJoinParam (class in auto_process_ngs.pipeliner) percent() (auto_process_ngs.utils.ProgressChecker method) (in module auto_process_ngs.barcodes.analysis) picard_collect_insert_size_metrics() (auto_process_ngs.mockqc.MockQCOutputs class method) picard_collect_insert_size_metrics_output() (in module auto_process_ngs.qc.outputs) Pipeline (class in auto_process_ngs.pipeliner) pipeline_name (auto_process_ngs.qc.cellranger.CellrangerCount property) (auto_process_ngs.qc.cellranger.CellrangerMulti property) PipelineCommand (class in auto_process_ngs.pipeliner)

PipelineCommandWrapper (class in auto_process_ngs.pipeliner) PipelineError PipelineFunctionTask (class in auto_process_ngs.pipeliner) PipelineParam (class in auto_process_ngs.pipeliner) PipelineScriptWrapper (class in auto_process_ngs.pipeliner) PipelineTask (class in auto_process_ngs.pipeliner) Plot (class in auto_process_ngs.qc.plots) plot() (auto_process_ngs.qc.fastqc.Fastqc method) (auto_process_ngs.qc.plots.Plot method) plot_range() (auto_process_ngs.qc.plots.Plot method) png (auto_process_ngs.qc.fastq_screen.Fastqscreen property) populate() (auto_process_ngs.analysis.AnalysisProject method) predict_outputs() (in module auto_process_ngs.samplesheet_utils) predict_samplesheet_outputs() (in module auto_process_ngs.commands.samplesheet_cmd) pretty_print_reads() (in module auto_process_ngs.qc.reporting) pretty_print_rows() (in module auto_process_ngs.utils) pretty_print_samples() (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv method) prettyPrintSamples() (auto_process_ngs.analysis.AnalysisProject method) print_metadata() (auto_process_ngs.auto_processor.AutoProcess method) print_params() (auto_process_ngs.auto_processor.AutoProcess method) print_values() (auto_process_ngs.auto_processor.AutoProcess method) probe_set (auto_process_ngs.qc.cellranger.CellrangerMulti property) probe_set_path (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv property) process_inputs() (in module auto_process_ngs.cli.run_qc) ProcessingQCReport (class in auto_process_ngs.bcl2fastq.reporting) ProgressChecker (class in auto_process_ngs.utils) ProjectMetadataFile (class in auto_process_ngs.metadata) protocol (auto_process_ngs.utils.Location property) publish_qc() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.publish_qc_cmd) PublishQCSchedulerReporter (class in auto_process_ngs.commands.publish_qc_cmd)

Q

qc_dir (auto_process_ngs.analysis.AnalysisProject property) qc_dirs (auto_process_ngs.analysis.AnalysisProject property) qc_info() (auto_process_ngs.analysis.AnalysisProject method) QCOutputs (class in auto_process_ngs.qc.outputs) QCPipeline (class in auto_process_ngs.qc.pipeline) QCProject (class in auto_process_ngs.qc.reporting) QCProtocol (class in auto_process_ngs.qc.protocols) QCProtocolError

QCProtocolParseSpecError QCReport (class in auto_process_ngs.qc.reporting) QCVerifier (class in auto_process_ngs.qc.verification) qualimap_rnaseq() (auto_process_ngs.mockqc.MockQCOutputs class method) (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) qualimap_rnaseq_output() (in module auto_process_ngs.qc.outputs) QualimapRnaseq (class in auto_process_ngs.qc.qualimap) quality_boxplot() (auto_process_ngs.qc.fastqc.Fastqc method) quote_spaces() (auto_process_ngs.pipeliner.PipelineCommand method)

R

r1 (auto_process_ngs.icell8.utils.ICell8ReadPair property) r2 (auto_process_ngs.icell8.utils.ICell8ReadPair property) range (auto_process_ngs.qc.seqlens.SeqLens property) rank_tasks() (auto_process_ngs.pipeliner.Pipeline method) raw (auto_process_ngs.stats.FastqStatistics property) raw_coverage_profile_along_genes_total (auto_process_ngs.qc.qualimap.QualimapRnaseq property) read (auto_process_ngs.icell8.utils.ICell8Read1 property) read() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) read_number (auto_process_ngs.stats.FastqStats property) readme() (in module auto_process_ngs.cli.auto_process) reads_genomic_origin (auto_process_ngs.qc.qualimap.QualimapRnaseq property) reads_per_lane() (auto_process_ngs.fastq_utils.FastqReadCounter static method) rebin_data() (auto_process_ngs.qc.plots.Plot method) reference (auto_process_ngs.barcodes.analysis.BarcodeGroup property) reference_data (auto_process_ngs.qc.cellranger.CellrangerCount property) (auto_process_ngs.qc.cellranger.CellrangerMulti property) reference_data_path (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv property) release() (auto_process_ngs.utils.FileLock method) remove_dir() (in module auto_process_ngs.fileops) remove_file() (in module auto_process_ngs.fileops) remove_index_fastqs() (in module auto_process_ngs.fastq_utils) remove_tmp_dir() (auto_process_ngs.auto_processor.AutoProcess method) rename() (in module auto_process_ngs.fileops) replace_with() (auto_process_ngs.pipeliner.PipelineParam method) report() (auto_process_ngs.pipeliner.Pipeline method) (auto_process_ngs.pipeliner.PipelineTask method) (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.report_cmd) (in module auto_process_ngs.icell8.atac) (in module auto_process_ngs.qc.reporting) report_additional_metrics() (auto_process_ngs.qc.reporting.QCReport method) report_barcodes() (in module auto_process_ngs.barcodes.analysis) report_basic_stats() (auto_process_ngs.stats.FastqStatistics method) report_comments() (auto_process_ngs.qc.reporting.QCReport method) report_concise() (in module auto_process_ngs.commands.report_cmd) report_diagnostics() (auto_process_ngs.pipeliner.PipelineTask method) report_extra_outputs() (auto_process_ngs.qc.reporting.QCReport method) report_failure() (auto_process_ngs.pipeliner.PipelineTask method) report_fastq_groups() (auto_process_ngs.qc.reporting.SampleQCReporter method) report_fastq_screens() (auto_process_ngs.qc.reporting.FastqQCReporter method) report_fastqc() (auto_process_ngs.qc.reporting.FastqQCReporter method) report_full_stats() (auto_process_ngs.stats.FastqStatistics method) report_genebody_coverage() (auto_process_ngs.qc.reporting.QCReport method) report_info() (in module auto_process_ngs.commands.report_cmd) report_insert_size_metrics() (auto_process_ngs.qc.reporting.QCReport method) report_metadata() (auto_process_ngs.qc.reporting.QCReport method) report_multiplexing_analyses() (auto_process_ngs.qc.reporting.QCReport method) report_multiqc() (auto_process_ngs.qc.reporting.QCReport method) report_per_lane_sample_stats() (auto_process_ngs.stats.FastqStatistics method) report_per_lane_summary_stats() (auto_process_ngs.stats.FastqStatistics method) report_processing_qc() (in module auto_process_ngs.commands.update_fastq_stats_cmd) report_processing_software() (auto_process_ngs.qc.reporting.QCReport method) report_program_versions() (auto_process_ngs.qc.reporting.FastqQCReporter method) report_projects() (in module auto_process_ngs.commands.report_cmd) report_qc() (in module auto_process_ngs.qc.utils) report_qc_software() (auto_process_ngs.qc.reporting.QCReport method)

report_sample() (auto_process_ngs.qc.reporting.QCReport method) report_settings() (auto_process_ngs.settings.Settings method) report_single_library_analyses() (auto_process_ngs.qc.reporting.QCReport method) report_status() (auto_process_ngs.qc.reporting.QCReport method) report_strandedness() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) report_summary() (in module auto_process_ngs.commands.report_cmd) report_text() (in module auto_process_ngs.pipeliner) ReportBarcodeAnalysis (class in auto_process_ngs.barcodes.pipeline) Reporter (class in auto_process_ngs.barcodes.analysis) ReportProcessing (class in auto_process_ngs.icell8.pipeline) ReportProcessingQC (class in auto_process_ngs.bcl2fastq.pipeline) ReportQC (class in auto_process_ngs.qc.pipeline) required_by() (auto_process_ngs.pipeliner.PipelineTask method) required_task_ids (auto_process_ngs.pipeliner.PipelineTask property) requires() (auto_process_ngs.pipeliner.PipelineTask method) requires_id() (auto_process_ngs.pipeliner.PipelineTask method) resolve_dependencies() (auto_process_ngs.pipeliner.PipelineTask method) resolve_parameter() (in module auto_process_ngs.pipeliner) resolve_undefined_params() (auto_process_ngs.settings.Settings method) resolving_dependencies (auto_process_ngs.pipeliner.PipelineTask property) restart() (auto_process_ngs.simple_scheduler.SchedulerJob method) RestoreBackupDirectory (class in auto_process_ngs.bcl2fastq.pipeline) result() (auto_process_ngs.pipeliner.PipelineFunctionTask method) results_txt (auto_process_ngs.qc.qualimap.QualimapRnaseq property) reverse (auto_process_ngs.qc.rseqc.InferExperiment property) reverse_complement() (in module auto_process_ngs.icell8.atac) rseqc_genebody_coverage() (auto_process_ngs.mockqc.MockQCOutputs class method) rseqc_genebody_coverage_output() (in module auto_process_ngs.qc.outputs) rseqc_infer_experiment() (auto_process_ngs.mockqc.MockQCOutputs class method) rsync() (auto_process_ngs.applications.general static method) run() (auto_process_ngs.barcodes.pipeline.AnalyseBarcodes method) (auto_process_ngs.bcl2fastq.pipeline.MakeFastqs method) (auto_process_ngs.icell8.pipeline.ICell8QCFilter method) (auto_process_ngs.pipeliner.Pipeline method) (auto_process_ngs.pipeliner.PipelineTask method) (auto_process_ngs.qc.pipeline.QCPipeline method) (auto_process_ngs.simple_scheduler.SimpleScheduler method) Run10xMkfastq (class in auto_process_ngs.bcl2fastq.pipeline) run_id (auto_process_ngs.auto_processor.AutoProcess property) (auto_process_ngs.qc.reporting.QCProject property) run_id() (in module auto_process_ngs.analysis) run_qc() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.run_qc_cmd) run_reference_id (auto_process_ngs.auto_processor.AutoProcess property) run_subprocess() (auto_process_ngs.command.Command method) RunBcl2Fastq (class in auto_process_ngs.bcl2fastq.pipeline) RunBclConvert (class in auto_process_ngs.bcl2fastq.pipeline) RunCellrangerCount (class in auto_process_ngs.qc.pipeline) RunCellrangerMulti (class in auto_process_ngs.qc.pipeline) RunFastQC (class in auto_process_ngs.qc.pipeline) RunFastqScreen (class in auto_process_ngs.qc.pipeline) RunFastqStrand (class in auto_process_ngs.qc.pipeline) runner_nslots (auto_process_ngs.pipeliner.PipelineTask property) runners (auto_process_ngs.pipeliner.Pipeline property) RunPicardCollectInsertSizeMetrics (class in auto_process_ngs.qc.pipeline) RunQualimapRnaseq (class in auto_process_ngs.qc.pipeline) RunRSeQCGenebodyCoverage (class in auto_process_ngs.qc.pipeline) RunRSeQCInferExperiment (class in auto_process_ngs.qc.pipeline)

S

sample() (auto_process_ngs.icell8.utils.ICell8WellList method) (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv method) sample_name (auto_process_ngs.qc.cellranger.CellrangerCount property) sample_names (auto_process_ngs.qc.cellranger.CellrangerMulti property) (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv property) sample_summary() (auto_process_ngs.analysis.AnalysisProject method) SampleQCReporter (class in auto_process_ngs.qc.reporting) samples() (auto_process_ngs.barcodes.analysis.SampleSheetBarcodes method) (auto_process_ngs.icell8.utils.ICell8WellList method) samples_in_multiple_projects() (auto_process_ngs.samplesheet_utils.SampleSheetLinter method) samples_with_multiple_barcodes() (auto_process_ngs.samplesheet_utils.SampleSheetLinter method) samplesheet() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.samplesheet_cmd) SampleSheetBarcodes (class in auto_process_ngs.barcodes.analysis) SampleSheetLinter (class in auto_process_ngs.samplesheet_utils) sanitize_css_string() (in module auto_process_ngs.docwriter) sanitize_name() (in module auto_process_ngs.pipeliner) (in module auto_process_ngs.qc.reporting) save() (auto_process_ngs.metadata.MetadataDict method) (auto_process_ngs.metadata.ProjectMetadataFile method) (auto_process_ngs.qc.plots.Plot method) (auto_process_ngs.settings.Settings method) save_data() (auto_process_ngs.auto_processor.AutoProcess method) save_metadata() (auto_process_ngs.auto_processor.AutoProcess method) save_parameters() (auto_process_ngs.auto_processor.AutoProcess method) scheduler_status() (auto_process_ngs.simple_scheduler.SchedulerReporter method) SchedulerCallback (class in auto_process_ngs.simple_scheduler) SchedulerException SchedulerGroup (class in auto_process_ngs.simple_scheduler) SchedulerJob (class in auto_process_ngs.simple_scheduler) SchedulerReporter (class in auto_process_ngs.simple_scheduler) SchedulerTimeout scp() (auto_process_ngs.applications.general static method) Section (class in auto_process_ngs.docwriter) sections (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv property) SeqLens (class in auto_process_ngs.qc.seqlens) seqlens() (auto_process_ngs.mockqc.MockQCOutputs class method) sequence_deduplication_percentage() (auto_process_ngs.qc.fastqc.FastqcData method) sequences (auto_process_ngs.barcodes.analysis.BarcodeGroup property) (auto_process_ngs.barcodes.splitter.BarcodeMatcher property) server (auto_process_ngs.utils.Location property) set() (auto_process_ngs.pipeliner.PipelineParam method) (auto_process_ngs.settings.Settings method) set_cell_count_for_project() (in module auto_process_ngs.qc.utils) set_debug() (in module auto_process_ngs.cli.auto_process) set_default_log_dir() (auto_process_ngs.qc.pipeline.QCPipeline method) set_group() (in module auto_process_ngs.fileops) set_group_command() (in module auto_process_ngs.fileops) set_log_dir() (auto_process_ngs.auto_processor.AutoProcess method) set_metadata() (auto_process_ngs.auto_processor.AutoProcess method) set_param() (auto_process_ngs.auto_processor.AutoProcess method) set_permissions() (in module auto_process_ngs.fileops) set_permissions_command() (in module auto_process_ngs.fileops) set_pixel() (auto_process_ngs.qc.plots.Plot method) set_primary_fastq_dir() (auto_process_ngs.analysis.AnalysisProject method) set_project() (in module auto_process_ngs.commands.samplesheet_cmd) set_sample_id() (in module auto_process_ngs.commands.samplesheet_cmd) set_sample_name() (in module auto_process_ngs.commands.samplesheet_cmd) set_samplesheet_column() (in module auto_process_ngs.samplesheet_utils) set_template() (auto_process_ngs.simple_scheduler.SchedulerReporter method) set_value() (auto_process_ngs.docwriter.Table method) SetCellCountFromCellranger (class in auto_process_ngs.qc.pipeline) Settings (class in auto_process_ngs.settings) setup() (auto_process_ngs.barcodes.pipeline.CountBarcodes method) (auto_process_ngs.barcodes.pipeline.ListBarcodeCountFiles method) (auto_process_ngs.barcodes.pipeline.LoadIlluminaData method) (auto_process_ngs.barcodes.pipeline.ReportBarcodeAnalysis method) (auto_process_ngs.barcodes.pipeline.SetupBarcodeAnalysisDirs method) (auto_process_ngs.bcl2fastq.pipeline.DemultiplexIcell8Atac method) (auto_process_ngs.bcl2fastq.pipeline.FastqStatistics method) (auto_process_ngs.bcl2fastq.pipeline.FetchPrimaryData method) (auto_process_ngs.bcl2fastq.pipeline.Get10xPackage method) (auto_process_ngs.bcl2fastq.pipeline.GetBasesMask10xMultiome method) (auto_process_ngs.bcl2fastq.pipeline.GetBasesMaskIcell8 method) (auto_process_ngs.bcl2fastq.pipeline.GetBasesMaskIcell8Atac method) (auto_process_ngs.bcl2fastq.pipeline.GetBcl2Fastq method) (auto_process_ngs.bcl2fastq.pipeline.GetBclConvert method) (auto_process_ngs.bcl2fastq.pipeline.IdentifyPlatform method) (auto_process_ngs.bcl2fastq.pipeline.MakeSampleSheet method) (auto_process_ngs.bcl2fastq.pipeline.MergeFastqDirs method) (auto_process_ngs.bcl2fastq.pipeline.MergeFastqs method) (auto_process_ngs.bcl2fastq.pipeline.ReportProcessingQC method) (auto_process_ngs.bcl2fastq.pipeline.RestoreBackupDirectory method) (auto_process_ngs.bcl2fastq.pipeline.Run10xMkfastq method) (auto_process_ngs.bcl2fastq.pipeline.RunBcl2Fastq method) (auto_process_ngs.bcl2fastq.pipeline.RunBclConvert method) (auto_process_ngs.icell8.pipeline.CheckICell8Barcodes method) (auto_process_ngs.icell8.pipeline.CleanupDirectory method) (auto_process_ngs.icell8.pipeline.CollectFiles method) (auto_process_ngs.icell8.pipeline.ConvertStatsToXLSX method) (auto_process_ngs.icell8.pipeline.FilterContaminatedReads method) (auto_process_ngs.icell8.pipeline.FilterICell8Fastqs method) (auto_process_ngs.icell8.pipeline.GetICell8Stats method) (auto_process_ngs.icell8.pipeline.GetReadsWithPolyGRegions method) (auto_process_ngs.icell8.pipeline.GroupFastqsByBarcode method) (auto_process_ngs.icell8.pipeline.GroupFastqsBySample method) (auto_process_ngs.icell8.pipeline.MergeBarcodeFastqs method) (auto_process_ngs.icell8.pipeline.MergeSampleFastqs method) (auto_process_ngs.icell8.pipeline.PairFastqs method) (auto_process_ngs.icell8.pipeline.ReportProcessing method) (auto_process_ngs.icell8.pipeline.SetupDirectories method) (auto_process_ngs.icell8.pipeline.SplitByBarcodes method) (auto_process_ngs.icell8.pipeline.SplitFastqsIntoBatches method) (auto_process_ngs.icell8.pipeline.TrimReads method) (auto_process_ngs.icell8.pipeline.UpdateProjectData method) (auto_process_ngs.pipeliner.PipelineTask method) (auto_process_ngs.qc.pipeline.CheckCellrangerCountOutputs method) (auto_process_ngs.qc.pipeline.CheckFastQCOutputs method) (auto_process_ngs.qc.pipeline.CheckFastqScreenOutputs method) (auto_process_ngs.qc.pipeline.CheckFastqStrandOutputs method) (auto_process_ngs.qc.pipeline.CollateInsertSizes method) (auto_process_ngs.qc.pipeline.ConvertGTFToBed method) (auto_process_ngs.qc.pipeline.DetermineRequired10xPackage method) (auto_process_ngs.qc.pipeline.GetBAMFiles method) (auto_process_ngs.qc.pipeline.GetCellrangerMultiConfig method) (auto_process_ngs.qc.pipeline.GetCellrangerReferenceData method) (auto_process_ngs.qc.pipeline.GetReferenceDataset method) (auto_process_ngs.qc.pipeline.GetSeqLengthStats method) (auto_process_ngs.qc.pipeline.GetSequenceDataFastqs method) (auto_process_ngs.qc.pipeline.GetSequenceDataSamples method) (auto_process_ngs.qc.pipeline.MakeCellrangerArcCountLibraries method) (auto_process_ngs.qc.pipeline.ReportQC method) (auto_process_ngs.qc.pipeline.RunCellrangerCount method) (auto_process_ngs.qc.pipeline.RunCellrangerMulti method) (auto_process_ngs.qc.pipeline.RunFastQC method) (auto_process_ngs.qc.pipeline.RunFastqScreen method) (auto_process_ngs.qc.pipeline.RunFastqStrand method) (auto_process_ngs.qc.pipeline.RunPicardCollectInsertSizeMetrics method) (auto_process_ngs.qc.pipeline.RunQualimapRnaseq method) (auto_process_ngs.qc.pipeline.RunRSeQCGenebodyCoverage method) (auto_process_ngs.qc.pipeline.RunRSeQCInferExperiment method) (auto_process_ngs.qc.pipeline.SetCellCountFromCellranger method) (auto_process_ngs.qc.pipeline.SetupFastqStrandConf method) (auto_process_ngs.qc.pipeline.SetupQCDirs method) (auto_process_ngs.qc.pipeline.SplitFastqsByLane method) (auto_process_ngs.qc.pipeline.UpdateQCMetadata method) (auto_process_ngs.qc.pipeline.VerifyFastqs method) (auto_process_ngs.qc.pipeline.VerifyQC method) (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.setup_cmd)

setup_analysis_dirs() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.setup_analysis_dirs_cmd) setup_qc_dir() (auto_process_ngs.analysis.AnalysisProject method) SetupBarcodeAnalysisDirs (class in auto_process_ngs.barcodes.pipeline) SetupDirectories (class in auto_process_ngs.icell8.pipeline) SetupFastqStrandConf (class in auto_process_ngs.qc.pipeline) SetupQCDirs (class in auto_process_ngs.qc.pipeline) show_dictionary() (in module auto_process_ngs.settings) simple() (auto_process_ngs.fastq_utils.FastqReadCounter static method) SimpleScheduler (class in auto_process_ngs.simple_scheduler) software_info() (auto_process_ngs.qc.reporting.QCProject method) sort_sample_names() (in module auto_process_ngs.utils) spaceranger_info() (in module auto_process_ngs.tenx.utils) split_fastq() (in module auto_process_ngs.icell8.atac) split_paired_end() (in module auto_process_ngs.barcodes.splitter) split_sample_name() (in module auto_process_ngs.analysis) split_sample_reference() (in module auto_process_ngs.analysis) split_single_end() (in module auto_process_ngs.barcodes.splitter) SplitAndFilterFastqPair (class in auto_process_ngs.icell8.pipeline) SplitByBarcodes (class in auto_process_ngs.icell8.pipeline) SplitFastqsByLane (class in auto_process_ngs.qc.pipeline) SplitFastqsIntoBatches (class in auto_process_ngs.icell8.pipeline) ssh_command() (auto_process_ngs.applications.general static method) STAR() (auto_process_ngs.indexes.IndexBuilder method) star_genome_generate_cmd() (in module auto_process_ngs.indexes) start() (auto_process_ngs.simple_scheduler.SchedulerJob method) start_scheduler() (auto_process_ngs.pipeliner.Pipeline method) stats (auto_process_ngs.qc.fastq_strand.Fastqstrand property) stderr (auto_process_ngs.pipeliner.PipelineTask property) stdout (auto_process_ngs.pipeliner.PipelineTask property) stop() (auto_process_ngs.simple_scheduler.SimpleScheduler method) stop_scheduler() (auto_process_ngs.pipeliner.Pipeline method) strandedness() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) stripe() (auto_process_ngs.qc.plots.Plot method) submit() (auto_process_ngs.simple_scheduler.SimpleScheduler method) subprocess_check_output() (auto_process_ngs.command.Command method) subset() (in module auto_process_ngs.bcl2fastq.pipeline) subsets (auto_process_ngs.bcl2fastq.pipeline.MakeFastqs property) summarise() (auto_process_ngs.qc.protocols.QCProtocol method) summary (auto_process_ngs.qc.fastqc.Fastqc property)

T

Table (class in auto_process_ngs.docwriter) Target (class in auto_process_ngs.docwriter) task_completed() (auto_process_ngs.pipeliner.PipelineTask method) task_list() (auto_process_ngs.pipeliner.Pipeline method) terminate() (auto_process_ngs.pipeliner.Pipeline method) (auto_process_ngs.pipeliner.PipelineTask method) title (auto_process_ngs.docwriter.Document property) (auto_process_ngs.docwriter.Section property)

tmp_dir() (in module auto_process_ngs.icell8.pipeline) ToggleButton (class in auto_process_ngs.qc.reporting) total_genes_detected (auto_process_ngs.tenx.metrics.MultiplexSummary property) TransferDataSchedulerReporter (class in auto_process_ngs.cli.transfer_data) TrimFastqPair (class in auto_process_ngs.icell8.pipeline) TrimReads (class in auto_process_ngs.icell8.pipeline) tss_enrichment_score (auto_process_ngs.tenx.metrics.AtacSummary property) txt (auto_process_ngs.qc.fastq_screen.Fastqscreen property) (auto_process_ngs.qc.fastq_strand.Fastqstrand property)

U

uadapterplot() (auto_process_ngs.qc.reporting.FastqQCReporter method) (in module auto_process_ngs.qc.plots) uboxplot() (auto_process_ngs.qc.reporting.FastqQCReporter method) (in module auto_process_ngs.qc.plots) ucoverageprofileplot() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) (in module auto_process_ngs.qc.plots) uduplicationplot() (auto_process_ngs.qc.reporting.FastqQCReporter method) (in module auto_process_ngs.qc.plots) ufastqcplot() (auto_process_ngs.qc.reporting.FastqQCReporter method) (in module auto_process_ngs.qc.plots) ugenomicoriginplot() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) (in module auto_process_ngs.qc.plots) uinsertsizeplot() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) (in module auto_process_ngs.qc.plots) umi (auto_process_ngs.icell8.utils.ICell8Read1 property) umi_quality (auto_process_ngs.icell8.utils.ICell8Read1 property) unstranded (auto_process_ngs.qc.rseqc.InferExperiment property) unzip() (in module auto_process_ngs.fileops) unzip_command() (in module auto_process_ngs.fileops) update() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.update_cmd) update_fastq_read_index() (in module auto_process_ngs.icell8.atac) update_fastq_stats() (in module auto_process_ngs.cli.auto_process) (in module auto_process_ngs.commands.update_fastq_stats_cmd) update_metadata() (auto_process_ngs.auto_processor.AutoProcess method)

update_multiplexing_analysis_table() (auto_process_ngs.qc.reporting.SampleQCReporter method) update_project() (auto_process_ngs.metadata.ProjectMetadataFile method) update_project_metadata_file() (auto_process_ngs.auto_processor.AutoProcess method) update_single_library_table() (auto_process_ngs.qc.reporting.SampleQCReporter method) update_summary_table() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) (auto_process_ngs.qc.reporting.SampleQCReporter method) UpdateAnalysisDir (class in auto_process_ngs.mock) UpdateAnalysisProject (class in auto_process_ngs.mock) updated (auto_process_ngs.pipeliner.PipelineTask property) UpdateProjectData (class in auto_process_ngs.icell8.pipeline) UpdateQCMetadata (class in auto_process_ngs.qc.pipeline) ureadcountplot() (auto_process_ngs.qc.reporting.FastqQCReporter method) (in module auto_process_ngs.qc.plots) url (auto_process_ngs.utils.Location property) uscreenplot() (auto_process_ngs.qc.reporting.FastqQCReporter method) (in module auto_process_ngs.qc.plots) use_fastq_dir() (auto_process_ngs.analysis.AnalysisProject method) use_qc_dir() (auto_process_ngs.analysis.AnalysisProject method) useqlenplot() (auto_process_ngs.qc.reporting.FastqQCReporter method) (in module auto_process_ngs.qc.plots) user (auto_process_ngs.utils.Location property) ustackedbar() (in module auto_process_ngs.qc.plots) ustrandednessplot() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) ustrandplot() (auto_process_ngs.qc.reporting.FastqGroupQCReporter method) (in module auto_process_ngs.qc.plots) uuid (auto_process_ngs.pipeliner.BaseParam property)

V

value (auto_process_ngs.pipeliner.FunctionParam property) (auto_process_ngs.pipeliner.PipelineParam property) vdj_reference_path (auto_process_ngs.tenx.cellplex.CellrangerMultiConfigCsv property) verify() (auto_process_ngs.qc.verification.QCVerifier method) verify_10x_pipeline() (auto_process_ngs.qc.verification.QCVerifier method) verify_env() (auto_process_ngs.conda.CondaWrapper method) verify_project() (in module auto_process_ngs.qc.verification) verify_qc() (in module auto_process_ngs.qc.utils) verify_qc_module() (auto_process_ngs.qc.verification.QCVerifier method) verify_run() (in module auto_process_ngs.bcl2fastq.pipeline) VerifyFastqs (class in auto_process_ngs.qc.pipeline)

VerifyQC (class in auto_process_ngs.qc.pipeline) version (auto_process_ngs.conda.CondaWrapper property) (auto_process_ngs.qc.cellranger.CellrangerCount property) (auto_process_ngs.qc.cellranger.CellrangerMulti property) (auto_process_ngs.qc.fastq_screen.Fastqscreen property) (auto_process_ngs.qc.fastq_strand.Fastqstrand property) (auto_process_ngs.qc.fastqc.Fastqc property) (auto_process_ngs.qc.fastqc.FastqcData property) (auto_process_ngs.tenx.metrics.AtacSummary property) view_samplesheet() (in module auto_process_ngs.commands.samplesheet_cmd) vline() (auto_process_ngs.qc.plots.Plot method)

W

wait() (auto_process_ngs.simple_scheduler.SchedulerGroup method) (auto_process_ngs.simple_scheduler.SchedulerJob method) (auto_process_ngs.simple_scheduler.SimpleScheduler method) wait_for() (auto_process_ngs.simple_scheduler.SimpleScheduler method) walk() (auto_process_ngs.samplesheet_utils.SampleSheetLinter method) warning() (auto_process_ngs.bcl2fastq.reporting.ProcessingQCReport method) WarningIcon (class in auto_process_ngs.docwriter) warnings (auto_process_ngs.qc.fastqc.FastqcSummary property) web_summary (auto_process_ngs.qc.cellranger.CellrangerCount property) web_summary() (auto_process_ngs.qc.cellranger.CellrangerMulti method)

working_dir (auto_process_ngs.pipeliner.Dispatcher property) write() (auto_process_ngs.barcodes.analysis.BarcodeCounter method) (auto_process_ngs.barcodes.analysis.Reporter method) (auto_process_ngs.docwriter.Document method) (auto_process_ngs.utils.BufferedOutputFiles method) (auto_process_ngs.utils.OutputFiles method) write_html() (auto_process_ngs.barcodes.analysis.Reporter method) write_libraries_csv() (auto_process_ngs.tenx.multiome.MultiomeLibraries method) write_script_file() (in module auto_process_ngs.utils) write_xls() (auto_process_ngs.barcodes.analysis.Reporter method)

Z

zcat_wc() (auto_process_ngs.fastq_utils.FastqReadCounter static method)

zip (auto_process_ngs.qc.fastqc.Fastqc property) ZipArchive (class in auto_process_ngs.utils)