V2

.gitignore

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+.claude/
+.smoke_test/
+.nextflow/
+.nextflow.log*
+work/

CHANGELOG.md

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+# Changelog
+
+This file contains all notable changes to Bambu-Pipe. 
+
+---
+
+## [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`s, 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