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TrESFlow: Changelog

The format is based on Keep a Changelog and this project follows Semantic Versioning.

v1.1.1 - 2026-08-26

Fixed

  • Fixed canonical BAM filtering when noncanonical reference entries are interspersed with canonical chromosomes, preventing invalid reference IDs and BAI indexing failures.

v1.1.0 - 2026-08-24

Added

  • Multi-FASTQ input support for ordered technical sequencing chunks using YAML sequences or comma-separated paths.
  • Input FASTQ provenance tracking for multi-file libraries.

Changed

  • DNA read groups distinguish AVITI run, flowcell, and lane while preserving the logical library across sequencing units.

Fixed

  • Multi-FASTQ samplesheet normalization and validation for YAML lists and comma-separated inputs.

v1.0.0 - 2026-08-18

First public TrESFlow release.

Added

  • Nextflow DSL2 workflow for joint TrES-seq RNA and DNA preprocessing.
  • Hierarchical YAML samplesheet supporting RNA-only, DNA-only, and multimodal samples.
  • Single- and dual-tagmentation DNA library support.
  • RNA STARsolo alignment and filtered-cell BAM/coverage outputs.
  • DNA alignment, duplicate marking, NoDup BAMs, and BigWig coverage tracks.
  • AVITI-aware optical duplicate handling with lane-level read groups.
  • Dual-tagmentation residual-linker artifact filtering.
  • FastQC, samtools QC, MultiQC, and the self-contained TrESFlow HTML QC report.
  • Read-retention, barcode-composition, library-complexity, and sequencing metrics.
  • Configurable resource profiles and runtime/work-directory handling.

Changed

  • Split FASTQ publication is optional while internal uncompressed FASTQs are used downstream.
  • RNA filtered BAM processing and canonical BAM validation were optimized to reduce redundant I/O.
  • RNA coverage generation was parallelized without changing coverage definitions.
  • Output structure was consolidated under rna_align/, dna_align/, TrES_Stats/, and pipeline_info/.

Fixed

  • RNA and DNA split-retention metric propagation.
  • RNA group routing for multiple sample-barcode groups.
  • DNA ligation-index handling for single versus dual tagmentation.
  • Picard MarkDuplicates performance regression caused by excessive read-group cardinality.
  • Canonical chromosome filtering and NoDup coverage consistency.