v2.1.0 - Sao Pablo

QPX and MuData Release

First introduction to QPX and MuData into quantmsdiann.

What's Changed

• Move input type validation before SDRF parsing by @ypriverol in #65
• Add --mzml_convert parameter for native Thermo .raw support by @ypriverol in #68
• Default local_input_type to raw and enforce supported local file formats by @Copilot in #64
• Minor update by @yueqixuan in #72
• Improve raw data file extension handling in input channel creation by @ypriverol in #69
• chore: nf-core 4.0.2 template sync by @ypriverol in #77
• feat: restrict --input to .sdrf.tsv extension by @ypriverol in #78
• feature: .wiff Dataset Support by @yueqixuan in #73
• Add optional PRIDE Archive download via pridepy by @ypriverol in #80
• Sync from master by @ypriverol in #81
• Claude/fix pr 82 q dwst by @ypriverol in #83
• fix: address GitHub issue for BlockedFlags by @yueqixuan in #84
• docs: add guide for reproducing DIA-NN GUI runs by @ypriverol in #88
• Integrate QPX Parquet and MuData export into workflow by @Shen-YuFei in #87
• Update sdrf-pipelines to 0.1.4 by @ypriverol in #89
• Fix QPX export: disable by default and require project_accession by @ypriverol in #90
• Update WIFF support and update documentation for QPX by @Shen-YuFei in #91
• Release 2.1.0 - Integration with wiff converter by @ypriverol in #82

New Contributors

• @Copilot made their first contribution in #64
• @Shen-YuFei made their first contribution in #87

Full Changelog: v2.0.0...v2.1.0

v2.0.0 - Rome

What's Changed

• Small patch to fix release CI/CD tests by @ypriverol in #35
• feat: v1.0.0 — robustness, DDA support, new params, InfinDIA, docs by @ypriverol in #32
• Support multiplexing by @yueqixuan in #37
• Update the quantms-utils and pmultiqc images by @yueqixuan in #46
• Fix/insilico log diann 2.3.2 by @ypriverol in #40
• feat: rename FDR params and expose matrix-level q-value controls by @ypriverol in #44
• feat: add DIA-NN scoring mode parameter (Generic/Proteoforms/Peptidoforms) by @ypriverol in #45
• refactor: centralize blocked flags + fix missing guards from PR #36 review by @ypriverol in #48
• chore: bump version to 2.0.0 (Rome) and update CHANGELOG by @ypriverol in #50
• Minor update by @yueqixuan in #52
• feat: add DIA-NN 2.5.0 support with model fine-tuning documentation by @ypriverol in #53
• feat: add optional FINE_TUNE_MODELS step for DL model fine-tuning by @ypriverol in #54
• fix by @yueqixuan in #56
• fix by @yueqixuan in #57
• New release 2.0.0 including dda workflow for quantmsdiann by @ypriverol in #36
• chore: update CHANGELOG for 2.0.0 and remove mkdocs/ by @ypriverol in #58
• Release 2.0.0 by @ypriverol in #59
• docs: add container building and HPC deployment guide by @ypriverol in #60
• Dev by @ypriverol in #61

Full Changelog: v1.0.0...v2.0.0

v1.0.0 - Cambridge

What's Changed

• extract DIA-NN workflow from quantms by @yueqixuan in #11
• Add Peptidoform Scoring Control by @yueqixuan in #13
• small changes by @yueqixuan in #14
• Refactoring ongoing for quantmsdiann - iteration one Remove MSStats postprocessing by @ypriverol in #12
• Improving the workflow image by @ypriverol in #16
• Add Synchro-PASEF / timsTOF Flags by @yueqixuan in #18
• Minor update by @yueqixuan in #20
• Refactor: extract calibration params to meta by @yueqixuan in #22
• fix by @yueqixuan in #23
• Refactor empirical log parsing logic by @yueqixuan in #24
• Minor changes in the sdrf-pipelines by @ypriverol in #19
• Minor updates by @yueqixuan in #28
• Minor update by @yueqixuan in #31
• Suppress protein inference warning in PRELIMINARY_ANALYSIS by @ypriverol in #29
• Add Bruker/timsTOF auto-calibration warning by @ypriverol in #30
• Remove unused logo by @yueqixuan in #33
• First release of quantmsdiann including new features previously no supported by @ypriverol in #27

New Contributors

• @yueqixuan made their first contribution in #11
• @ypriverol made their first contribution in #12

Full Changelog: https://github.com/bigbio/quantmsdiann/commits/v1.0.0