v0.9-beta

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 CompressedCharacterLists, 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