Introduction

• Salient Features
  • Streamlined
  • Maintaining project structure
  • Easy modification or addition of rules
  • One-select running of popular workflows
  • Easy resource maintenance
  • Re-attempts for known issues or errors
• Executing the Pipeline
  • Installing dependencies
  • Setting up profiles
  • Executing Pipeline

Getting Started

• Understanding Snakemake workflows
• A basic pipeline
  • Setting up

Understanding the Pipeline

• Overview of the Pipeline
• Wildcard Processing
  • List of samples
• Selectable Modules
  • Module description
• Sub-Snakemake workflows

Advanced Tutorials

• Demultiplex pooled snRNA seq datasets
  • Pipeline overwiew
  • Preparing target files
  • Configuration File
  • Project-specific changes to rules
  • Changes to executor script

Reference

• helper_py_scripts
  • create_Feat_Barc module
  • create_aggregate_matrix module
  • create_filter_perPool_vcf module
  • create_h5ad_from_bustools module
  • create_h5ad_from_calico_solo module
  • create_inp_cellSNP module
  • create_inp_cellrangerArcCount module
  • create_inp_splitBam_consolidated module
  • create_wet_lab_info module
  • demul_samples module
  • demultiplex_helper_funcs module
  • qtltools_plot_samples_wo_gt_multiprocess module
  • update_logs module
• Glossary

Development News

• Changelog
  • Pipeline & Workflow
  • Demultiplexing (demultiplex.smk / demul_samples.py)
  • Genotype Demultiplexing (genotype_demux.smk)
  • BAM Splitting (split_bams.smk)
  • Target Production (produce_targets.smk)
  • Logging & QC (update_logs.py / run_update_logs.sh)
  • Wet Lab Info (create_wet_lab_info.py)
  • Configuration (new_config.yaml)
  • Alignment Support
  • Miscellaneous
• TODO
  • Architecture & Design
  • Compatibility
  • Demultiplexing
  • cellranger
  • STARsolo
  • Code Quality
  • Experimental / Future
  • Documentation & Schemas
• API Reference
  • update_logs
  • demul_samples
  • create_Feat_Barc
  • create_inp_cellSNP
  • create_wet_lab_info
  • create_aggregate_matrix
  • demultiplex_helper_funcs
  • create_h5ad_from_bustools
  • create_filter_perPool_vcf
  • create_h5ad_from_calico_solo
  • create_inp_cellrangerArcCount
  • create_inp_splitBam_consolidated
  • qtltools_plot_samples_wo_gt_multiprocess

Indices and tables

• Index

• Module Index

• Search Page