This repository contains the CWL and YML files necessary to run the BD Genomics Rhapsody Analysis Pipeline locally.
To obtain the files, click on Downloads in the left navigation panel, and then Download repository.
For more details on how to use these files, see the BD Genomics Analysis Setup User Guide (Doc ID: 47383).
BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline:
- Added Sample_Tag_ReadsPerCell.csv to Multiplex Output
- Optimized pipeline in various steps for memory usage
- Fixed bug in status determination for UMI_Adjusted_Stats.csv file
BD Rhapsody™ Targeted Analysis Pipeline:
- Updated Targets section in Metrics_Summary.csv to calculate metrics based on targets detected in putative cells only
- Removed Clustering Analysis and outputs
BD Rhapsody™ WTA Analysis Pipeline:
- Added support for BD™ AbSeq libraries
- Removed Targets section in Metrics_Summary.csv for WTA only libraries
- Removed Pct_Error_Reads and Error_Depth in UMI_Adjusted_Stats.csv, which are not applicable to WTA only libraries
- Added BD Rhapsody™ WTA Analysis Pipeline
- Fixed bug that can cause stalling when zero putative cells were identified
- Fixed bug that affected runs using Disable Refined Putative Cell Calling option
- Increased memory limits for GetDataTable and Metrics
- Fixed bug associated with "No Multiplex" option on SBG
- Uses fewer resources in AddToSam step.
- Added new options for putative cell determination:
- Exact Cell Count: Set a specific number of cells as putative, based on those with the highest error-corrected read count
- Disable Refined Putative Cell Calling: Determine putative cells using only the basic algorithm
- Updated to Python 3
- Updated alignment defaults (minor molecule count changes expected)
- Local install only - CWL files are bundled into one file
- Added support for BD Single-cell multiplexing kit – Mouse Immune
- Updated various filtering thresholds to support sequencing runs with shorter read length
- Deprecated pipeline input – BAM input
- Fixed bug in Quality Filter (minor metrics changes expected)
- Optimized pipeline (computationally faster, more scalable to support larger input data size, and better logging)
- Added support for BD™ AbSeq assay
- Added support for BD™ single-cell multiplexing kit - Mouse Immune
- New pipeline input - AbSeq Reference
- New pipeline outputs - Unfiltered cell-gene data tables
- Updated Metrics_Summary.csv to support metrics from multiple sequencing libraries
- Updated Recursive Substitution Error Correction (RSEC) algorithm (minor molecule count changes expected)
- Optimized pipeline to run faster
- Added support for BD Single-cell multiplexing kit - Human
- Improved pipeline speed by deleting large temp files
- Removed network requirement when running locally
- bug fix for the wrong docker image name - Dec 13, 2017