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Developers' API documentation
=============================

.. toctree::
   :maxdepth: 2

   analysis
   applications
   apps
   auto_processor
   barcodes
   barcodes_analysis
   barcodes_pipeline
   barcodes_splitter
   bcl2fastq
   bcl2fastq_apps
   bcl2fastq_pipeline
   bcl2fastq_protocols
   bcl2fastq_reporting
   bcl2fastq_utils
   cli
   cli_auto_process
   cli_build_index
   cli_fetch_data
   cli_reportqc
   cli_run_qc
   cli_transfer_data
   command
   commands
   commands_analyse_barcodes_cmd
   commands_archive_cmd
   commands_clone_cmd
   commands_import_project_cmd
   commands_make_fastqs_cmd
   commands_merge_fastq_dirs_cmd
   commands_publish_qc_cmd
   commands_report_cmd
   commands_run_qc_cmd
   commands_samplesheet_cmd
   commands_setup_analysis_dirs_cmd
   commands_setup_cmd
   commands_update_cmd
   commands_update_fastq_stats_cmd
   conda
   config
   conftest
   css_rules
   decorators
   docs
   docwriter
   exceptions
   fastq_utils
   fileops
   indexes
   metadata
   mock
   mock10xdata
   mockqc
   mockqcdata
   pipeliner
   qc
   qc_apps
   qc_apps_cellranger
   qc_apps_fastq_screen
   qc_apps_fastq_strand
   qc_apps_fastqc
   qc_apps_picard
   qc_apps_qualimap
   qc_apps_rseqc
   qc_apps_seqlens
   qc_fastq_stats
   qc_modules
   qc_modules_cellranger_arc_count
   qc_modules_cellranger_atac_count
   qc_modules_cellranger_count
   qc_modules_cellranger_multi
   qc_modules_fastq_screen
   qc_modules_fastqc
   qc_modules_multiqc
   qc_modules_picard_insert_size_metrics
   qc_modules_qualimap_rnaseq
   qc_modules_rseqc_genebody_coverage
   qc_modules_rseqc_infer_experiment
   qc_modules_sequence_lengths
   qc_modules_strandedness
   qc_outputs
   qc_pipeline
   qc_plots
   qc_protocols
   qc_qc_modules
   qc_reporting
   qc_utils
   qc_verification
   samplesheet_utils
   settings
   simple_scheduler
   stats
   tenx
   tenx_cellplex
   tenx_metrics
   tenx_multiome
   tenx_utils
   utils