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Changelog

This file contains all notable changes to Bambu-Pipe.

[v0.10.1] - 2026-08-26

Added

  • --loupe_alignment for Visium Spatial Gene Expression samples, taking the manual alignment .json exported after fiducial alignment and tissue detection in Loupe Browser. Required for visium-v* samples
    • Out-of-tissue barcodes are filtered from the BAM before transcript discovery and quantification
    • Introduce the VISIUM_BUILD_TISSUE_POSITIONS module, which builds the tissue positions file for visium-v* samples; the spatial metadata in this file is attached to the colData of the SummarizedExperiment objects
    • Loupe alignment example (examples/loupe_alignment_visium_example.json), used by the test_visium smoke test
  • CB/UB tags in aligned BAM files (minimap2 -y), carrying the barcode and UMI from the FASTQ header comments

Changed

  • The spatial metadata attached to Visium SummarizedExperiment objects now follows the Space Ranger tissue positions format (barcode, in_tissue, array_row, array_col, pxl_row_in_fullres, pxl_col_in_fullres), replacing the x_coordinate/y_coordinate columns
  • FILTER_BARCODED_BAM moved to modules/prepare_input/shared/ and is used by both the standard Visium and Visium HD workflows; it now fails when no reads remain after filtering
  • User-supplied BAM files must carry the barcode and UMI in the CB/UB tags; barcodes encoded in the read name are no longer supported

Fixed

  • flexiplex-filter's knee detection could discard most in-tissue barcodes for Visium samples; the inflection search now covers the whole barcode rank curve (-u 0) for visium-v* chemistries

[v0.10.0] - 2026-08-17

Added

  • Visium HD workflow (--visium_hd), run as a single sample from a Spaceranger-aligned, barcode-tagged BAM
    • Transcript discovery and read-to-transcript assignment at the native 2 µm resolution, with counts aggregated to every bin listed in --bins
    • --barcode_mappings for the Spaceranger barcode_mappings.parquet, used to assign 2 µm spots to bins
    • Out-of-tissue reads filtered from the BAM using the 2 µm tissue_positions.parquet
    • Spatially aware clustering with Banksy (--banksy, --banksy_lambda, --banksy_k_geom), or gene expression alone
    • --clustering_bin to select the resolution to cluster at; cluster labels are expanded back to 2 µm spots for quantification
    • Spot-level quantification at every resolution under --quantification_mode EM
    • test_visium_hd smoke test profile with synthetic example data
  • --manual_clustering to restart the pipeline from cluster assignments generated outside the pipeline, for both standard and Visium HD runs
  • test_sc_quant_data and test_visium_hd_quant_data smoke test profiles covering the manual clustering restart
  • Self-hosted bambu and seurat container images published to ghcr.io/goekelab, built by the build_container.yml GitHub Actions workflow
  • Shared R helpers in bin/ for transcript discovery, Seurat object creation, count saving, and cluster mapping

Changed

  • Renamed --resolution to --seurat_resolution
  • Renamed the --quantification_mode option EM_clusters to clusteredEM, matching the bambu.singlecell API
  • quant_data.rds and extended_annotations.rds are now always published to intermediate_R/, so a manual clustering run can restart from them
  • Seurat objects are built from the published count directories and Bambu's colData instead of the SummarizedExperiment
  • clusters.rds is now a named vector of id -> cluster label, replacing the per-sample list of CompressedCharacterList
  • Cluster-level quantification moved into a single module shared by the standard and Visium HD workflows
  • Restructured modules into standard/, visium_hd/, and shared/ directories
  • Smoke tests now run on pull request and manual dispatch only, with in-progress runs cancelled on a new push

[v0.9.1] - 2026-05-20

Added

  • Harmony batch correction for multi-sample Seurat clustering
  • Processing of CB/UB tagged custom BAM files
  • GitHub Actions workflow to run smoke test on push and pull request to main and devel branches

Changed

  • Upgraded pipeline to support Nextflow version 26.04.0 and above

[v0.9-beta] - 2026-05-11

Added

  • Quality score filtering with Chopper
  • Primer removal with Cutadapt
  • Reverse complement FASTQ utility script (bin/reverse_complement_fastq.py) to enable stranded alignment in minimap2
  • Automatic extraction of 10x barcodes and spatial coordinates from the Spaceranger container
  • Support for multiple sample analysis using Nextflow parallelisation
  • Modularised codebase into discrete modules and subworkflows (modules/bambu/, modules/alignment/, modules/prepare_input_standard/)
  • External 10x config asset files for barcode coordinates, adapter sequences, and flank sequences
  • params block centralising all pipeline parameters (previously defined in main.nf)
  • process block with dynamic retry strategy
  • Resource labels for CPU, memory, and time
  • HPC execution profile (conf/) to support parallelisation on high performance computing systems
  • Minimal end-to-end smoke test (conf/test.config)
  • Manifest block with author and version metadata
  • Emit software versions in a .yml file
  • Input validation via lib/Validation.groovy
  • quantification_mode parameter to control quantification strategy (no_quant, EM, EM_clusters)
  • Seurat clustering as a dedicated process (SEURAT_CLUSTERING) for cluster-based EM quantification
  • Joint clustering across all samples on a combined gene counts matrix (previously per-sample)
  • Cluster output restructured to an ordered list of CompressedCharacterList, one per sample in quantData order (previously a flat single CCL mixing all samples)
  • SEURAT_CLUSTERING now takes gene counts matrix and sample names as inputs instead of the full quantData object
  • clusterCells helper inlined into the process (previously sourced from bin/utilityFunctions.R)
  • early_stop_stage parameter to terminate the pipeline after BAM or RDS generation

Changed

  • Migration to Wave community containers (previously root-level Dockerfile)
  • Removed deprecated parameters
  • Removed hardcoded values and redundant code
  • Simplified input logic using a single samplesheet
  • Enhanced input validation check

[v0.1-beta] - 2025-05-19

Added

  • Initial pipeline release