Getting started
Pipeline stages
Post-processing
Single cell data
Spatial data
Helpers
Control files
Outputs
Reference Documentation
auto_process
Developer Documentation
auto_process_ngs.analysis
auto_process_ngs.applications
auto_process_ngs.apps
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.apps
auto_process_ngs.bcl2fastq.pipeline
auto_process_ngs.bcl2fastq.protocols
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.fetch_data
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.docs
auto_process_ngs.docwriter
auto_process_ngs.exceptions
auto_process_ngs.fastq_utils
auto_process_ngs.fileops
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.apps
auto_process_ngs.qc.apps.cellranger
auto_process_ngs.qc.apps.fastq_screen
auto_process_ngs.qc.apps.fastq_strand
auto_process_ngs.qc.apps.fastqc
auto_process_ngs.qc.apps.picard
auto_process_ngs.qc.apps.qualimap
auto_process_ngs.qc.apps.rseqc
auto_process_ngs.qc.apps.seqlens
auto_process_ngs.qc.fastq_stats
auto_process_ngs.qc.modules
auto_process_ngs.qc.modules.cellranger_arc_count
auto_process_ngs.qc.modules.cellranger_atac_count
auto_process_ngs.qc.modules.cellranger_count
auto_process_ngs.qc.modules.cellranger_multi
auto_process_ngs.qc.modules.fastq_screen
auto_process_ngs.qc.modules.fastqc
auto_process_ngs.qc.modules.multiqc
auto_process_ngs.qc.modules.picard_insert_size_metrics
auto_process_ngs.qc.modules.qualimap_rnaseq
auto_process_ngs.qc.modules.rseqc_genebody_coverage
auto_process_ngs.qc.modules.rseqc_infer_experiment
auto_process_ngs.qc.modules.sequence_lengths
auto_process_ngs.qc.modules.strandedness
auto_process_ngs.qc.outputs
auto_process_ngs.qc.pipeline
auto_process_ngs.qc.plots
auto_process_ngs.qc.protocols
auto_process_ngs.qc.qc_modules
auto_process_ngs.qc.reporting
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