Dev

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.7.0] bigbio/quantms - [] -
+## [1.7.0] bigbio/quantms - [08/01/2026] - [Caracas]
 
 ### `Added`
 
@@ -12,9 +12,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
-- [627](https://github.com/bigbio/quantms/pull/627) Move thermorawfileparser from local to bigbio nf-core
+- [627](https://github.com/bigbio/quantms/pull/627) Move thermorawfileparser and onsite modules from local to bigbio/nf-modules
 - [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) Changed enable_diann_mztab default from true to false. 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. See the [Migration Guide](docs/usage.md#migrating-from-luciphor_-to-onsite_-parameters-version-170) in the documentation for a complete parameter mapping table and migration instructions.
+
 ## [1.6.0] bigbio/quantms - [13/08/2025] - Munich
 
 ### `Added`

README.md

@@ -34,7 +34,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser))
 2. Peptide identification using [`comet`](https://uwpr.github.io/Comet/) and/or [`msgf+`](https://github.com/MSGFPlus/msgfplus)
-3. (Optional) Add extra PSM features using [`ms2rescore`](https://github.com/compomics/ms2rescore)
+3. (Optional) Add extra PSM features using [`quantms-rescoring`](https://github.com/bigbio/quantms-rescoring)
 4. Re-scoring peptide identifications [`percolator`](https://github.com/percolator/percolator)
 5. Peptide identification FDR [`openms fdr tool`](https://github.com/bigbio/quantms/blob/HEAD/modules/local/openms/false_discovery_rate/main.nf)
 6. Modification localization [`onsite`](https://github.com/bigbio/onsite)
@@ -47,7 +47,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser))
 2. Peptide identification using [`comet`](https://uwpr.github.io/Comet/) and/or [`msgf+`](https://github.com/MSGFPlus/msgfplus)
-3. (Optional) Add extra PSM features using [`ms2rescore`](https://github.com/compomics/ms2rescore)
+3. (Optional) Add extra PSM features using [`quantms-rescoring`](https://github.com/bigbio/quantms-rescoring)
 4. Re-scoring peptide identifications [`percolator`](https://github.com/percolator/percolator)
 5. Peptide identification FDR [`openms fdr tool`](https://github.com/bigbio/quantms/blob/HEAD/modules/local/openms/false_discovery_rate/main.nf)
 6. Modification localization [`onsite`](https://github.com/bigbio/onsite)

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/bigbio/quantms/releases/tag/1.6.0" target="_blank">bigbio/quantms</a>
+  This report has been generated by the <a href="https://github.com/bigbio/quantms/releases/tag/1.7.0" target="_blank">bigbio/quantms</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://docs.quantms.org/en/latest" target="_blank">documentation</a>.
 report_section_order:

conf/dev.config

@@ -24,6 +24,6 @@ process {
 
     // ONSITE uses its own container (not OpenMS thirdparty)
     withName: '.*:PHOSPHO_SCORING:ONSITE' {
-        container = {"${ ( workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ) && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pyonsite:0.0.1--pyhdfd78af_0' : 'quay.io/biocontainers/pyonsite:0.0.1--pyhdfd78af_0' }"}
+        container = {"${ ( workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ) && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pyonsite:0.0.2--pyhdfd78af_0' : 'quay.io/biocontainers/pyonsite:0.0.2--pyhdfd78af_0' }"}
     }
 }