Developers’ API documentation
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
DemultiplexIcell8Atac
FastqStatistics
FetchPrimaryData
Get10xPackage
GetBasesMask10xMultiome
GetBasesMaskIcell8
GetBasesMaskIcell8Atac
GetBcl2Fastq
GetBclConvert
IdentifyPlatform
MakeFastqs
MakeSampleSheet
MergeFastqDirs
MergeFastqs
ReportProcessingQC
RestoreBackupDirectory
Run10xMkfastq
RunBcl2Fastq
RunBclConvert
create_placeholder_fastqs()
subset()
verify_run()
auto_process_ngs.bcl2fastq.reporting
auto_process_ngs.bcl2fastq.utils
auto_process_ngs.cli
auto_process_ngs.cli.auto_process
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.reportqc
auto_process_ngs.cli.run_qc
InfoAction
add_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_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
BatchFastqs
CheckICell8Barcodes
CleanupDirectory
CollectFiles
ConcatFastqs
ContaminantFilterFastqPair
ConvertStatsToXLSX
FilterContaminatedReads
FilterICell8Fastqs
FilterPolyGReads
GetICell8PolyGStats
GetICell8Stats
GetReadsWithPolyGRegions
GroupFastqsByBarcode
GroupFastqsBySample
ICell8FinalReporting
ICell8QCFilter
ICell8Statistics
MergeBarcodeFastqs
MergeSampleFastqs
PairFastqs
ReportProcessing
SetupDirectories
SplitAndFilterFastqPair
SplitByBarcodes
SplitFastqsIntoBatches
TrimFastqPair
TrimReads
UpdateProjectData
convert_to_xlsx()
tmp_dir()
auto_process_ngs.icell8.utils
auto_process_ngs.indexes
auto_process_ngs.metadata
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
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()
make_conda_env()
report_text()
resolve_parameter()
sanitize_name()
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
ExtraOutputs
QCOutputs
cellranger_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.picard
auto_process_ngs.qc.pipeline
CheckCellrangerCountOutputs
CheckFastQCOutputs
CheckFastqScreenOutputs
CheckFastqStrandOutputs
CollateInsertSizes
ConvertGTFToBed
DetermineRequired10xPackage
GetBAMFiles
GetCellrangerMultiConfig
GetCellrangerReferenceData
GetReferenceDataset
GetSeqLengthStats
GetSequenceDataFastqs
GetSequenceDataSamples
MakeCellrangerArcCountLibraries
QCPipeline
ReportQC
RunCellrangerCount
RunCellrangerMulti
RunFastQC
RunFastqScreen
RunFastqStrand
RunPicardCollectInsertSizeMetrics
RunQualimapRnaseq
RunRSeQCGenebodyCoverage
RunRSeQCInferExperiment
SetCellCountFromCellranger
SetupFastqStrandConf
SetupQCDirs
SplitFastqsByLane
UpdateQCMetadata
VerifyFastqs
VerifyQC
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
BufferedOutputFiles
FileLock
FileLockError
Location
OutputFiles
ProgressChecker
ZipArchive
edit_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()