Developers’ API documentation

• auto_process_ngs.analysis
  • AnalysisDir
  • AnalysisFastq
  • AnalysisProject
  • AnalysisSample
  • copy_analysis_project()
  • locate_project()
  • locate_project_info_file()
  • locate_run()
  • match_run_id()
  • run_id()
  • run_reference_id()
  • split_sample_name()
  • split_sample_reference()
• auto_process_ngs.applications
  • fetch_application_data()
  • identify_application()
  • match_application()
  • score_match()
  • split_library_type()
• auto_process_ngs.apps
  • general
• auto_process_ngs.auto_processor
  • AutoProcess
• auto_process_ngs.barcodes
• auto_process_ngs.barcodes.analysis
  • BarcodeCounter
  • BarcodeGroup
  • Reporter
  • SampleSheetBarcodes
  • detect_barcodes_warnings()
  • make_title()
  • percent()
  • report_barcodes()
• auto_process_ngs.barcodes.pipeline
  • AnalyseBarcodes
  • CountBarcodes
  • ListBarcodeCountFiles
  • LoadIlluminaData
  • ReportBarcodeAnalysis
  • SetupBarcodeAnalysisDirs
• auto_process_ngs.barcodes.splitter
  • BarcodeMatcher
  • HammingLookup
  • HammingMetrics
  • get_fastqs_from_dir()
  • split_paired_end()
  • split_single_end()
• auto_process_ngs.bcl2fastq
• auto_process_ngs.bcl2fastq.apps
  • bcl2fastq2()
  • bclconvert()
  • configureBclToFastq()
• auto_process_ngs.bcl2fastq.pipeline
  • FastqStatistics
  • FetchPrimaryData
  • Get10xPackage
  • GetBasesMask
  • GetBcl2Fastq
  • GetBclConvert
  • IdentifyPlatform
  • MakeFastqs
  • MakeSampleSheet
  • MergeFastqDirs
  • MergeFastqs
  • ReportProcessingQC
  • RestoreBackupDirectory
  • Run10xMkfastq
  • RunBcl2Fastq
  • RunBclConvert
  • SeqLengthStatistics
  • create_placeholder_fastqs()
  • subset()
  • verify_run()
• auto_process_ngs.bcl2fastq.protocols
• auto_process_ngs.bcl2fastq.reporting
  • ProcessingQCReport
  • detect_processing_qc_warnings()
• auto_process_ngs.bcl2fastq.utils
  • available_bcl2fastq_versions()
  • bases_mask_is_valid()
  • bcl_to_fastq_info()
  • bclconvert_info()
  • check_barcode_collisions()
  • convert_bases_mask_to_override_cycles()
  • get_bases_mask()
  • get_nmismatches()
  • get_required_samplesheet_format()
  • get_run_config()
  • get_sequencer_platform()
  • make_custom_sample_sheet()
• auto_process_ngs.cli
• auto_process_ngs.cli.auto_process
  • AutoProcess
  • add_analyse_barcodes_command()
  • add_archive_command()
  • add_clone_command()
  • add_config_command()
  • add_import_project_command()
  • add_info_command()
  • add_make_fastqs_command()
  • add_merge_fastq_dirs_command()
  • add_metadata_command()
  • add_params_command()
  • add_publish_qc_command()
  • add_readme_command()
  • add_report_command()
  • add_run_qc_command()
  • add_samplesheet_command()
  • add_setup_analysis_dirs_command()
  • add_setup_command()
  • add_update_command()
  • add_update_fastq_stats_command()
  • analyse_barcodes()
  • archive()
  • clone()
  • config()
  • import_project()
  • info()
  • main()
  • make_fastqs()
  • merge_fastq_dirs()
  • metadata()
  • params()
  • publish_qc()
  • readme()
  • report()
  • run_qc()
  • samplesheet()
  • set_debug()
  • setup()
  • setup_analysis_dirs()
  • update()
  • update_fastq_stats()
• auto_process_ngs.cli.build_index
• auto_process_ngs.cli.fetch_data
  • copy_dir_contents()
  • copy_file()
  • main()
  • run_command()
  • run_rsync()
• auto_process_ngs.cli.reportqc
• auto_process_ngs.cli.run_qc
  • InfoAction
  • add_10x_options()
  • add_advanced_options()
  • add_conda_options()
  • add_custom_protocol_options()
  • add_debug_options()
  • add_deprecated_options()
  • add_job_control_options()
  • add_metadata_options()
  • add_pipeline_options()
  • add_reference_data_options()
  • add_reporting_options()
  • announce()
  • build_10x_multi_config()
  • cleanup_atexit()
  • display_info()
  • get_applications()
  • get_execution_environment()
  • main()
  • process_inputs()
• auto_process_ngs.cli.transfer_data
  • TransferData
  • TransferDataSchedulerReporter
  • get_templates_dir()
  • main()
• auto_process_ngs.command
  • Command
• auto_process_ngs.commands
• auto_process_ngs.commands.analyse_barcodes_cmd
  • analyse_barcodes()
• auto_process_ngs.commands.archive_cmd
  • archive()
• auto_process_ngs.commands.clone_cmd
  • clone()
• auto_process_ngs.commands.import_project_cmd
  • import_project()
• auto_process_ngs.commands.make_fastqs_cmd
  • make_fastqs()
• auto_process_ngs.commands.merge_fastq_dirs_cmd
  • merge_fastq_dirs()
• auto_process_ngs.commands.publish_qc_cmd
  • PublishQCSchedulerReporter
  • publish_qc()
• auto_process_ngs.commands.report_cmd
  • default_value()
  • fetch_value()
  • get_multiplexed_samples()
  • report()
  • report_concise()
  • report_info()
  • report_projects()
  • report_summary()
• auto_process_ngs.commands.run_qc_cmd
  • run_qc()
• auto_process_ngs.commands.samplesheet_cmd
  • edit_samplesheet()
  • import_samplesheet()
  • predict_samplesheet_outputs()
  • samplesheet()
  • set_project()
  • set_sample_id()
  • set_sample_name()
  • summarise_samplesheet_outputs()
  • view_samplesheet()
• auto_process_ngs.commands.setup_analysis_dirs_cmd
  • setup_analysis_dirs()
• auto_process_ngs.commands.setup_cmd
  • setup()
• auto_process_ngs.commands.update_cmd
  • update()
• auto_process_ngs.commands.update_fastq_stats_cmd
  • fastq_statistics()
  • get_absolute_file_path()
  • report_processing_qc()
  • update_fastq_stats()
• auto_process_ngs.conda
  • CondaCreateEnvError
  • CondaWrapper
  • CondaWrapperError
  • make_conda_env_name()
• auto_process_ngs.config
  • Config
  • NullValue
• auto_process_ngs.conftest
• auto_process_ngs.css_rules
• auto_process_ngs.decorators
  • add_command()
• auto_process_ngs.docs
  • ExampleQCPlots
  • RstGridTable
  • RstSimpleTable
  • generate_api_docs()
  • generate_applications_table()
  • generate_command_docs()
  • generate_fq_protocols_for_apps()
  • generate_fq_protocols_tbl()
  • generate_qc_protocols_tbl()
  • generate_utility_docs()
  • get_help_text()
  • get_modules()
• auto_process_ngs.docwriter
  • Document
  • DocumentIcon
  • DownloadIcon
  • Img
  • Link
  • LinkIcon
  • List
  • Para
  • Section
  • Table
  • Target
  • WarningIcon
  • escape_quotes()
  • sanitize_css_string()
• auto_process_ngs.exceptions
  • MissingParameterFileException
• auto_process_ngs.fastq_utils
  • BaseFastqAttrs
  • FastqReadCounter
  • IlluminaFastqAttrs
  • assign_barcodes_single_end()
  • build_custom_fastq_attrs_regex()
  • get_custom_fastqattrs_class()
  • get_read_count()
  • get_read_number()
  • group_fastqs_by_name()
  • pair_fastqs()
  • pair_fastqs_by_name()
  • remove_index_fastqs()
• auto_process_ngs.fileops
  • copy()
  • copy_command()
  • copytree()
  • copytree_command()
  • disk_usage()
  • exists()
  • isdir()
  • listdir()
  • mkdir()
  • quote_spaces()
  • remove_dir()
  • remove_file()
  • rename()
  • set_group()
  • set_group_command()
  • set_permissions()
  • set_permissions_command()
  • unzip()
  • unzip_command()
• auto_process_ngs.indexes
  • IndexBuilder
  • bowtie2_build_cmd()
  • bowtie_build_cmd()
  • star_genome_generate_cmd()
• auto_process_ngs.metadata
  • AnalysisDirMetadata
  • AnalysisDirParameters
  • AnalysisProjectInfo
  • AnalysisProjectQCDirInfo
  • MetadataDict
  • ProjectMetadataFile
  • item_to_name()
  • name_to_item()
• auto_process_ngs.mock
  • DirectoryUpdater
  • Mock10xPackageExe
  • MockAnalysisDir
  • MockAnalysisDirFactory
  • MockAnalysisProject
  • MockBcl2fastq2Exe
  • MockBclConvertExe
  • MockBowtie2Build
  • MockBowtieBuild
  • MockCellrangerExe
  • MockConda
  • MockFastQC
  • MockFastqScreen
  • MockFastqStrandPy
  • MockGtf2bed
  • MockMultiQC
  • MockPicard
  • MockQualimap
  • MockRSeQC
  • MockSamtools
  • MockSeqtk
  • MockStar
  • UpdateAnalysisDir
  • UpdateAnalysisProject
  • make_mock_analysis_project()
  • make_mock_bcl2fastq2_output()
• auto_process_ngs.mock10xdata
• auto_process_ngs.mockqc
  • MockQCOutputs
  • make_10x_multi_config_file()
  • make_mock_qc_dir()
• auto_process_ngs.mockqcdata
• auto_process_ngs.pipeliner
  • Overview
  • Defining tasks: examples
  • Running scripts from within tasks
  • Defining task outputs
  • Using task output as input to another task
  • Task working directory isolation
  • Specialised task input/output classes
  • Running Python functions as tasks
  • Building and running a pipeline
  • Defining relationships between tasks
  • Scheduling and running jobs
  • Specifying job runners for tasks
  • Dynamically setting number of CPUs/threads via job runners
  • Dealing with stdout and stderr from tasks
  • Handling failed tasks in pipelines
  • Executing pipeline commands in batches
  • Setting pipeline parameters at execution time
  • Built-in parameters
  • Defining execution environment for a task: runners, modules & conda
  • Defining outputs from a pipeline
  • Enabling conda to create task environments automatically
  • A note on PipelineCommand and PipelineCommandWrapper
  • Advanced pipeline construction: combining pipelines
  • BaseParam
  • Capturing
  • Dispatcher
  • FileCollector
  • FunctionParam
  • ListParam
  • PathExistsParam
  • PathJoinParam
  • Pipeline
  • PipelineCommand
  • PipelineCommandWrapper
  • PipelineError
  • PipelineFunctionTask
  • PipelineParam
  • PipelineScriptWrapper
  • PipelineTask
  • check_conda_env()
  • collect_files()
  • format_compute_time()
  • make_conda_env()
  • report_text()
  • resolve_parameter()
  • sanitize_name()
• auto_process_ngs.qc
• auto_process_ngs.qc.apps
• auto_process_ngs.qc.apps.cellranger
  • CellrangerCount
  • CellrangerMulti
  • cellranger_arc_count_output()
  • cellranger_atac_count_output()
  • cellranger_count_output()
  • cellranger_multi_output()
  • extract_path_data()
  • fetch_cellranger_multi_output_dirs()
• auto_process_ngs.qc.apps.fastq_screen
  • Fastqscreen
  • LEGACY_SCREENS
  • fastq_screen_output_files()
• auto_process_ngs.qc.apps.fastq_strand
  • Fastqstrand
  • build_fastq_strand_conf()
  • fastq_strand_output()
  • logger
• auto_process_ngs.qc.apps.fastqc
  • Fastqc
  • FastqcData
  • FastqcSummary
  • SEQUENCE_DEDUP_CUTOFFS
  • fastqc_output_files()
• auto_process_ngs.qc.apps.picard
  • CollectInsertSizeMetrics
  • logger
  • picard_collect_insert_size_metrics_output()
• auto_process_ngs.qc.apps.qualimap
  • QualimapRnaseq
  • qualimap_rnaseq_output()
• auto_process_ngs.qc.apps.rseqc
  • InferExperiment
  • logger
  • rseqc_genebody_coverage_output()
• auto_process_ngs.qc.apps.seqlens
  • SeqLens
  • get_sequence_lengths()
• auto_process_ngs.qc.fastq_stats
  • FastqQualityStats
• auto_process_ngs.qc.modules
  • QCDir
  • QCModule
• auto_process_ngs.qc.modules.cellranger_arc_count
  • CellrangerArcCount
• auto_process_ngs.qc.modules.cellranger_atac_count
  • CellrangerAtacCount
• auto_process_ngs.qc.modules.cellranger_count
  • CellrangerCount
  • CheckCellrangerCountOutputs
  • DetermineRequired10xPackage
  • GetCellrangerReferenceData
  • MakeCellrangerArcCountLibraries
  • RunCellrangerCount
  • add_cellranger_count()
  • check_cellranger_arc_count_outputs()
  • check_cellranger_atac_count_outputs()
  • check_cellranger_count_outputs()
  • filter_10x_pipelines()
  • verify_10x_pipeline()
• auto_process_ngs.qc.modules.cellranger_multi
  • CellrangerMulti
  • GetCellrangerMultiConfigs
  • RunCellrangerMulti
  • expected_outputs()
• auto_process_ngs.qc.modules.fastq_screen
  • CheckFastqScreenOutputs
  • FastqScreen
  • RunFastqScreen
  • check_fastq_screen_outputs()
• auto_process_ngs.qc.modules.fastqc
  • CheckFastQCOutputs
  • Fastqc
  • RunFastQC
  • check_fastqc_outputs()
• auto_process_ngs.qc.modules.multiqc
  • Multiqc
• auto_process_ngs.qc.modules.picard_insert_size_metrics
  • CollateInsertSizes
  • PicardInsertSizeMetrics
  • RunPicardCollectInsertSizeMetrics
• auto_process_ngs.qc.modules.qualimap_rnaseq
  • QualimapRnaseq
  • RunQualimapRnaseq
• auto_process_ngs.qc.modules.rseqc_genebody_coverage
  • RseqcGenebodyCoverage
  • RunRSeQCGenebodyCoverage
• auto_process_ngs.qc.modules.rseqc_infer_experiment
  • RseqcInferExperiment
  • RunRSeQCInferExperiment
• auto_process_ngs.qc.modules.sequence_lengths
  • GetSeqLengthStats
  • SequenceLengths
• auto_process_ngs.qc.modules.strandedness
  • CheckFastqStrandOutputs
  • RunFastqStrand
  • SetupFastqStrandConf
  • Strandedness
  • check_fastq_strand_outputs()
• auto_process_ngs.qc.outputs
  • ExtraOutputs
  • QCOutputs
• auto_process_ngs.qc.pipeline
  • ConvertGTFToBed
  • GetBAMFiles
  • GetReferenceDataset
  • GetSequenceDataFastqs
  • GetSequenceDataSamples
  • QCPipeline
  • ReportQC
  • RunMultiQC
  • Set10xCellCount
  • SetupQCDirs
  • SplitFastqsByLane
  • UpdateQCMetadata
  • VerifyFastqs
  • VerifyQC
• auto_process_ngs.qc.plots
  • Plot
  • encode_png()
  • make_plot()
  • uadapterplot()
  • uboxplot()
  • ucoverageprofileplot()
  • uduplicationplot()
  • ufastqcplot()
  • ugenomicoriginplot()
  • uinsertsizeplot()
  • ureadcountplot()
  • uscreenplot()
  • useqlenplot()
  • ustackedbar()
  • ustrandplot()
• auto_process_ngs.qc.protocols
  • QCProtocol
  • QCProtocolError
  • QCProtocolParseSpecError
  • determine_qc_protocol()
  • determine_qc_protocol_from_metadata()
  • fetch_protocol_definition()
  • parse_protocol_spec()
  • parse_qc_module_spec()
• auto_process_ngs.qc.qc_modules
• auto_process_ngs.qc.reporting
  • Overview
  • Adding support for new metadata
  • Adding support for new QC outputs
  • FastqGroupQCReporter
  • FastqQCReporter
  • ProcessingSoftwareTable
  • ProjectMetadataTable
  • QCProject
  • QCReport
  • QCSoftwareTable
  • SampleQCReporter
  • ToggleButton
  • get_static_dir()
  • report()
  • sanitize_name()
• auto_process_ngs.qc.utils
  • filter_fastqs()
  • get_bam_basename()
  • get_bam_samplename()
  • get_seq_data_samples()
  • read_versions_file()
  • report_qc()
  • set_cell_count_for_project()
  • verify_qc()
• auto_process_ngs.qc.verification
  • QCVerifier
  • verify_project()
• auto_process_ngs.samplesheet_utils
  • SampleSheetLinter
  • barcode_is_10xgenomics()
  • barcode_is_valid()
  • check_and_warn()
  • get_close_names()
  • has_invalid_characters()
  • predict_outputs()
  • set_samplesheet_column()
  • summarise_outputs()
• auto_process_ngs.settings
  • GenericSettings
  • Settings
  • fetch_reference_data()
  • get_config_dir()
  • get_install_dir()
  • jobrunner()
  • locate_auto_process_settings_file()
  • locate_settings_file()
  • path()
  • show_dictionary()
• auto_process_ngs.simple_scheduler
  • SchedulerCallback
  • SchedulerException
  • SchedulerGroup
  • SchedulerJob
  • SchedulerReporter
  • SchedulerTimeout
  • SimpleScheduler
  • cleanup_atexit()
  • date_and_time()
  • default_scheduler_reporter()
• auto_process_ngs.stats
  • FastqStatistics
  • FastqStats
  • collect_fastq_data()
• auto_process_ngs.tenx
• auto_process_ngs.tenx.cellplex
  • CellrangerMultiConfigCsv
• auto_process_ngs.tenx.metrics
  • AtacSummary
  • GexSummary
  • MetricsSummary
  • MissingMetricError
  • MultiomeSummary
  • MultiplexSummary
• auto_process_ngs.tenx.multiome
  • MultiomeLibraries
• auto_process_ngs.tenx.utils
  • add_cellranger_args()
  • cellranger_info()
  • flow_cell_id()
  • has_10x_indices()
  • has_chromium_sc_indices()
  • make_multi_config_template()
  • make_qc_summary_html()
  • spaceranger_info()
• auto_process_ngs.utils
  • BufferedOutputFiles
  • FileLock
  • FileLockError
  • Location
  • OutputFiles
  • ProgressChecker
  • ZipArchive
  • ZipMaker
  • check_required_version()
  • edit_file()
  • fetch_file()
  • find_executables()
  • get_numbered_subdir()
  • get_organism_list()
  • normalise_organism_name()
  • paginate()
  • parse_samplesheet_spec()
  • parse_version()
  • parse_version_requirement()
  • pretty_print_reads()
  • pretty_print_rows()
  • sort_sample_names()
  • write_script_file()