22
33All notable changes to the aa-tRNA-seq pipeline are documented in this file.
44
5- The format is based on [ Keep a Changelog] ( https://keepachangelog.com/en/1.0.0/ ) .
6-
7- ## [ Unreleased]
5+ ## Unreleased
86
97### Added
108- Optional WarpDemuX barcode demultiplexing support for pooled/multiplexed sequencing runs (#74 )
@@ -16,7 +14,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
1614- Updated README to use pixi instead of conda (#72 )
1715- Normalized file permissions across repository
1816
19- ## [ 0.6.0 ] - 2025-11-07
17+ ## 2025-11-07
2018
2119### Added
2220- Claude Code session start hook for automated development setup (#69 )
@@ -27,7 +25,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
2725- Prefer pandas over polars for stability on some cluster nodes
2826- Reduced Remora logging level
2927
30- ## [ 0.5.0 ] - 2025-06-22
28+ ## 2025-06-22
3129
3230### Added
3331- LSF-specific cluster configuration (#63 )
@@ -37,7 +35,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
3735- Reduced and made optional dorado verbosity
3836- Downgraded numpy to fix remora stats compatibility
3937
40- ## [ 0.4.0 ] - 2025-03-16
38+ ## 2025-03-16
4139
4240### Added
4341- Modkit integration for RNA modification analysis (#59 )
@@ -58,7 +56,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
5856### Fixed
5957- Restored ` -v ` option in dorado for proper verbosity control
6058
61- ## [ 0.3.0 ] - 2025-01-08
59+ ## 2025-01-08
6260
6361### Added
6462- Rule for calculating CPM of charged/uncharged tRNAs (#28 )
@@ -74,7 +72,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
7472### Fixed
7573- Actually use the threshold value in classification
7674
77- ## [ 0.2.0 ] - 2024-08-13
75+ ## 2024-08-13
7876
7977### Added
8078- Alignment filtering capabilities with configurable parameters (#13 )
@@ -95,7 +93,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
9593- Dropped redundant summary align stats (#14 )
9694- Added 'pod5' to list of possible pod5 directories
9795
98- ## [ 0.1.0 ] - 2024-05-19
96+ ## 2024-05-19
9997
10098### Added
10199- Support for merging multiple sequencing runs per sample
@@ -115,7 +113,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
115113- Keep additional BAM flags (e.g., pi) during processing (#1 )
116114- Use -T → -C options to preserve all BAM tags from dorado
117115
118- ## [ 0.0.1 ] - 2024-02-07
116+ ## 2024-02-07
119117
120118### Added
121119- Initial pipeline release
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