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docs: remove version numbers from changelog
Use dates only since there are no git tags. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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CHANGELOG.md

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All notable changes to the aa-tRNA-seq pipeline are documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
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## [Unreleased]
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## Unreleased
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### Added
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- Optional WarpDemuX barcode demultiplexing support for pooled/multiplexed sequencing runs (#74)
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- Updated README to use pixi instead of conda (#72)
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- Normalized file permissions across repository
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## [0.6.0] - 2025-11-07
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## 2025-11-07
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- Claude Code session start hook for automated development setup (#69)
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- Prefer pandas over polars for stability on some cluster nodes
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- Reduced Remora logging level
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## [0.5.0] - 2025-06-22
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## 2025-06-22
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- LSF-specific cluster configuration (#63)
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- Reduced and made optional dorado verbosity
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- Downgraded numpy to fix remora stats compatibility
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## [0.4.0] - 2025-03-16
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## 2025-03-16
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- Modkit integration for RNA modification analysis (#59)
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### Fixed
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- Restored `-v` option in dorado for proper verbosity control
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## [0.3.0] - 2025-01-08
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## 2025-01-08
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- Rule for calculating CPM of charged/uncharged tRNAs (#28)
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### Fixed
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- Actually use the threshold value in classification
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## [0.2.0] - 2024-08-13
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## 2024-08-13
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- Alignment filtering capabilities with configurable parameters (#13)
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- Dropped redundant summary align stats (#14)
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- Added 'pod5' to list of possible pod5 directories
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## [0.1.0] - 2024-05-19
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## 2024-05-19
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- Support for merging multiple sequencing runs per sample
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- Keep additional BAM flags (e.g., pi) during processing (#1)
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- Use -T → -C options to preserve all BAM tags from dorado
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## [0.0.1] - 2024-02-07
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## 2024-02-07
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- Initial pipeline release

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