feat: add DIA-NN 2.5.0 support with model fine-tuning documentation#53
Merged
feat: add DIA-NN 2.5.0 support with model fine-tuning documentation#53
Conversation
- New v2_5_0.config version profile (ghcr.io/bigbio/diann:2.5.0) - Add diann_v2_5_0 profile to nextflow.config - Block --parent flag in BlockedFlags.groovy COMMON list (container-managed, overriding breaks model discovery) - Document fine-tuning workflow in docs/usage.md: - How to generate tuning libraries - How to fine-tune RT/IM/fragment models - How to use fine-tuned models via --extra_args - Update version tables in docs/usage.md and AGENTS.md New DIA-NN 2.5.0 CLI flags (passable via --extra_args): --tokens, --rt-model, --fr-model, --im-model (model selection) --aa-eq (amino acid equivalence for reannotation) --tune-lib, --tune-rt, --tune-im, --tune-fr (fine-tuning) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
|
Important Review skippedAuto reviews are disabled on base/target branches other than the default branch. Please check the settings in the CodeRabbit UI or the ⚙️ Run configurationConfiguration used: defaults Review profile: CHILL Plan: Pro Run ID: You can disable this status message by setting the Use the checkbox below for a quick retry:
✨ Finishing Touches🧪 Generate unit tests (beta)
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
Document all new DIA-NN 2.5.0 flags available via --extra_args: model selection (--tokens, --rt-model, --fr-model, --im-model), fine-tuning (--tune-lib, --tune-rt, --tune-im, --tune-fr, etc.), and --aa-eq for amino acid equivalence. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
|
Add aa_eq param (default: false) that maps to DIA-NN's --aa-eq flag. When enabled, I&L, Q&E, N&D are treated as equivalent amino acids during reannotation — essential for entrapment FDR benchmarks. - Added to nextflow.config, nextflow_schema.json, docs/parameters.md - Passed to all 5 DIA-NN modules - Added to BlockedFlags.groovy COMMON list (pipeline-managed) - Moved from "via extra_args" to proper pipeline parameter in docs Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
… for Vadim Rewrite the fine-tuning documentation to: - Explain what tokens/dict.txt are (neural network encoding of modifications) - Clarify that --tune-lib cannot be combined with --gen-spec-lib (separate DIA-NN invocations, confirmed in DIA-NN #1499) - Document the full two-run workflow with concrete commands - Propose the future integrated FINE_TUNE_MODELS step with a question for @vdemichev about the right integration point Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
diann_v2_5_0version profile (ghcr.io/bigbio/diann:2.5.0)--parentflag inBlockedFlags.groovyCOMMON list (container-managed model path)docs/usage.mddocs/usage.mdandAGENTS.mdDIA-NN 2.5.0 highlights
--tokens,--rt-model,--fr-model,--im-model)--tune-lib,--tune-rt,--tune-im,--tune-fr)--aa-eqfor amino acid equivalence in reannotation (useful for entrapment FDR benchmarks)Fine-tuning documentation
Added a complete section explaining:
--extra_argsContainer PR
Companion PR: bigbio/quantms-containers#11
🤖 Generated with Claude Code