Merge pull request #635 from ypriverol/dev

small changes for release

Author: ypriverol

CHANGELOG.md

@@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [627](https://github.com/bigbio/quantms/pull/627) Move thermorawfileparser from local to bigbio nf-core
 - [629](https://github.com/bigbio/quantms/pull/629) Update quantms-rescoring to 0.0.13 to support transfer learning
 - [615](https://github.com/bigbio/quantms/pull/615) Update quantms-utils 0.0.24 and pmultiqc 0.0.39
+- [614](https://github.com/bigbio/quantms/pull/614) enable_diann_mztab from true to false as default. For DIA pipelines the mzTab will not be generated unless specified by a parameter `--enable_diann_mztab true`.
+- [635](https://github.com/bigbio/quantms/pull/635) Minimum Nextflow version requirement updated to `>=25.04.0`
 
 ### `Fixed`
 
@@ -28,6 +30,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updated pyonsite==0.0.2
 - Updated quantms-utils==0.0.24
 
+### `Deprecations`
+
+- [626](https://github.com/bigbio/quantms/pull/626) Removed luciphor-specific parameters: `luciphor_neutral_losses`, `luciphor_decoy_mass`, `luciphor_decoy_neutral_losses`. These have been replaced with onsite parameters: `onsite_neutral_losses`, `onsite_decoy_mass`, `onsite_decoy_neutral_losses`. The new onsite module provides support for multiple PTM localization algorithms (AScore, PhosphoRS, and LucXor) with unified parameter naming.
+
 ## [1.6.0] bigbio/quantms - [13/08/2025] - Munich
 
 ### `Added`

modules/local/utils/msrescore_features/main.nf

@@ -48,13 +48,15 @@ process MSRESCORE_FEATURES {
         // ms2pip only supports Da unit
         ms2_tolerance_unit = 'Da'
         ms2_tolerance = params.ms2features_tolerance
-        if (meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('da')) {
+        def fragment_unit_lower = meta['fragmentmasstoleranceunit'].toLowerCase()
+        if (fragment_unit_lower.endsWith('da')) {
             ms2_tolerance = meta['fragmentmasstolerance']
-        } else if (params.ms2features_tolerance_unit == 'ppm') {
-            log.info "Warning: MS2pip only supports Da unit. Using default from config!"
-            ms2_tolerance = 0.05
+        } else if (fragment_unit_lower == 'ppm' || params.ms2features_tolerance_unit == 'ppm') {
+            log.warn "Warning: MS2pip only supports Da unit. Using default from config!"
+            ms2_tolerance = params.ms2features_tolerance
         } else {
-            log.info "Warning: MS2pip only supports Da unit. Using default from config!"
+            log.warn "Warning: MS2pip only supports Da unit. Fragment mass tolerance unit '${meta['fragmentmasstoleranceunit']}' is not supported. Using default from config! In the future, please use 'Da' or 'ppm'."
+            ms2_tolerance = params.ms2features_tolerance
         }
     }