Developers’ API documentation
auto_process_ngs.analysisauto_process_ngs.applicationsauto_process_ngs.auto_processorauto_process_ngs.barcodesauto_process_ngs.barcodes.analysisauto_process_ngs.barcodes.pipelineauto_process_ngs.barcodes.splitterauto_process_ngs.bcl2fastqauto_process_ngs.bcl2fastq.pipelineDemultiplexIcell8AtacFastqStatisticsFetchPrimaryDataGet10xPackageGetBasesMask10xMultiomeGetBasesMaskIcell8GetBasesMaskIcell8AtacGetBcl2FastqGetBclConvertIdentifyPlatformMakeFastqsMakeSampleSheetMergeFastqDirsMergeFastqsReportProcessingQCRestoreBackupDirectoryRun10xMkfastqRunBcl2FastqRunBclConvertcreate_placeholder_fastqs()subset()verify_run()
auto_process_ngs.bcl2fastq.reportingauto_process_ngs.bcl2fastq.utilsauto_process_ngs.cliauto_process_ngs.cli.auto_processadd_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_indexauto_process_ngs.cli.reportqcauto_process_ngs.cli.run_qcInfoActionadd_10x_options()add_advanced_options()add_conda_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()cleanup_atexit()display_info()get_execution_environment()process_inputs()
auto_process_ngs.cli.transfer_dataauto_process_ngs.commandauto_process_ngs.commandsauto_process_ngs.commands.analyse_barcodes_cmdauto_process_ngs.commands.archive_cmdauto_process_ngs.commands.clone_cmdauto_process_ngs.commands.import_project_cmdauto_process_ngs.commands.make_fastqs_cmdauto_process_ngs.commands.merge_fastq_dirs_cmdauto_process_ngs.commands.publish_qc_cmdauto_process_ngs.commands.report_cmdauto_process_ngs.commands.run_qc_cmdauto_process_ngs.commands.samplesheet_cmdauto_process_ngs.commands.setup_analysis_dirs_cmdauto_process_ngs.commands.setup_cmdauto_process_ngs.commands.update_cmdauto_process_ngs.commands.update_fastq_stats_cmdauto_process_ngs.condaauto_process_ngs.configauto_process_ngs.conftestauto_process_ngs.css_rulesauto_process_ngs.decoratorsauto_process_ngs.docwriterauto_process_ngs.exceptionsauto_process_ngs.fastq_utilsauto_process_ngs.fileopsauto_process_ngs.icell8auto_process_ngs.icell8.atacauto_process_ngs.icell8.constantsauto_process_ngs.icell8.pipelineBatchFastqsCheckICell8BarcodesCleanupDirectoryCollectFilesConcatFastqsContaminantFilterFastqPairConvertStatsToXLSXFilterContaminatedReadsFilterICell8FastqsFilterPolyGReadsGetICell8PolyGStatsGetICell8StatsGetReadsWithPolyGRegionsGroupFastqsByBarcodeGroupFastqsBySampleICell8FinalReportingICell8QCFilterICell8StatisticsMergeBarcodeFastqsMergeSampleFastqsPairFastqsReportProcessingSetupDirectoriesSplitAndFilterFastqPairSplitByBarcodesSplitFastqsIntoBatchesTrimFastqPairTrimReadsUpdateProjectDataconvert_to_xlsx()tmp_dir()
auto_process_ngs.icell8.utilsauto_process_ngs.indexesauto_process_ngs.metadataauto_process_ngs.mockDirectoryUpdaterMock10xPackageExeMockAnalysisDirMockAnalysisDirFactoryMockAnalysisProjectMockBcl2fastq2ExeMockBclConvertExeMockBowtie2BuildMockBowtieBuildMockCellrangerExeMockCondaMockFastQCMockFastqScreenMockFastqStrandPyMockGtf2bedMockMultiQCMockPicardMockQualimapMockRSeQCMockSamtoolsMockSeqtkMockStarUpdateAnalysisDirUpdateAnalysisProjectmake_mock_analysis_project()make_mock_bcl2fastq2_output()
auto_process_ngs.mock10xdataauto_process_ngs.mockqcauto_process_ngs.mockqcdataauto_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
BaseParamCapturingDispatcherFileCollectorFunctionParamListParamPathExistsParamPathJoinParamPipelinePipelineCommandPipelineCommandWrapperPipelineErrorPipelineFunctionTaskPipelineParamPipelineScriptWrapperPipelineTaskcheck_conda_env()collect_files()make_conda_env()report_text()resolve_parameter()sanitize_name()
auto_process_ngs.qcauto_process_ngs.qc.cellrangerauto_process_ngs.qc.constantsauto_process_ngs.qc.fastq_screenauto_process_ngs.qc.fastq_statsauto_process_ngs.qc.fastq_strandauto_process_ngs.qc.fastqcauto_process_ngs.qc.outputsExtraOutputsQCOutputscellranger_arc_count_output()cellranger_atac_count_output()cellranger_count_output()cellranger_multi_output()check_cellranger_arc_count_outputs()check_cellranger_atac_count_outputs()check_cellranger_count_outputs()check_fastq_screen_outputs()check_fastq_strand_outputs()check_fastqc_outputs()fastq_screen_output()fastq_strand_output()fastqc_output()picard_collect_insert_size_metrics_output()qualimap_rnaseq_output()rseqc_genebody_coverage_output()
auto_process_ngs.qc.picardauto_process_ngs.qc.pipelineCheckCellrangerCountOutputsCheckFastQCOutputsCheckFastqScreenOutputsCheckFastqStrandOutputsCollateInsertSizesConvertGTFToBedDetermineRequired10xPackageGetBAMFilesGetCellrangerMultiConfigGetCellrangerReferenceDataGetReferenceDatasetGetSeqLengthStatsGetSequenceDataFastqsGetSequenceDataSamplesMakeCellrangerArcCountLibrariesQCPipelineReportQCRunCellrangerCountRunCellrangerMultiRunFastQCRunFastqScreenRunFastqStrandRunPicardCollectInsertSizeMetricsRunQualimapRnaseqRunRSeQCGenebodyCoverageRunRSeQCInferExperimentSetCellCountFromCellrangerSetupFastqStrandConfSetupQCDirsSplitFastqsByLaneUpdateQCMetadataVerifyFastqsVerifyQC
auto_process_ngs.qc.plotsauto_process_ngs.qc.protocolsauto_process_ngs.qc.qualimapauto_process_ngs.qc.reportingauto_process_ngs.qc.rseqcauto_process_ngs.qc.seqlensauto_process_ngs.qc.utilsauto_process_ngs.qc.verificationauto_process_ngs.samplesheet_utilsauto_process_ngs.settingsauto_process_ngs.simple_schedulerauto_process_ngs.statsauto_process_ngs.tenxauto_process_ngs.tenx.cellplexauto_process_ngs.tenx.metricsauto_process_ngs.tenx.multiomeauto_process_ngs.tenx.utilsauto_process_ngs.utilsBufferedOutputFilesFileLockFileLockErrorLocationOutputFilesProgressCheckerZipArchiveedit_file()fetch_file()find_executables()get_numbered_subdir()get_organism_list()normalise_organism_name()paginate()parse_samplesheet_spec()parse_version()pretty_print_rows()sort_sample_names()write_script_file()