Dev

.nf-core.yml

@@ -33,4 +33,4 @@ template:
   name: quantms
   org: bigbio
   outdir: .
-  version: 1.8.0dev
+  version: 1.8.0

CHANGELOG.md

@@ -3,7 +3,44 @@
 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).
 
-## [1.8.0] bigbio/quantms - [Unreleased]
+## [1.8.0] bigbio/quantms - [23/06/2026] - [Guangzhou]
+
+### `Added`
+
+- [#690](https://github.com/bigbio/quantms/pull/690) Expose `fdr_conservative` parameter to control FDR estimation formula (Keich & Noble 2025)
+- [#694](https://github.com/bigbio/quantms/pull/694) Expose Biosaur2 as alternative feature seeding algorithm for LFQ via `lfq_seeding_algorithm` parameter
+- [#623](https://github.com/bigbio/quantms/pull/623) Add support for `.dia` file format and improve file format documentation
+
+### `Changed`
+
+- [#639](https://github.com/bigbio/quantms/pull/639) **BREAKING: Deprecated OpenMS experimental design format**: The pipeline now only accepts SDRF files as input. All input files are treated as SDRF regardless of file extension. Supported extensions: `.sdrf`, `.tsv`, `.csv`.
+- [#651](https://github.com/bigbio/quantms/pull/651) Remove redundant SDRF-derived parameters: 4 parameters (`acquisition_method`, `labelling_type`, `enzyme`, `fixed_mods`) are now read exclusively from SDRF files
+- [#644](https://github.com/bigbio/quantms/pull/644) Update pipeline for Nextflow 26 strict syntax compatibility
+- [#641](https://github.com/bigbio/quantms/pull/641) Enable `ext.args` support in GENERATE_CFG module for nf-core standard compliance
+- [#660](https://github.com/bigbio/quantms/pull/660) Refactor DIA-NN parameter handling for extended module validation
+- [#676](https://github.com/bigbio/quantms/pull/676) Fix `.d` file support and multiple Nextflow 26 compatibility issues
+- [#686](https://github.com/bigbio/quantms/pull/686) Update test configurations to fetch SDRF and FASTA files from maintained repository
+- [#687](https://github.com/bigbio/quantms/pull/687) Migrate thermorawfileparser module from local to bigbio/nf-modules
+- [#709](https://github.com/bigbio/quantms/pull/709) Update onsite module for improved PTM localization
+- [#690](https://github.com/bigbio/quantms/pull/690), [#694](https://github.com/bigbio/quantms/pull/694) OpenMS tooling improvements including FDR conservative formula and Biosaur2 feature seeding
+
+### `Fixed`
+
+- [#689](https://github.com/bigbio/quantms/pull/689) Fix typo in openms_peak_picker processOption value (`inmermory` → `inmemory`)
+- [#699](https://github.com/bigbio/quantms/pull/699) Fix Comet version reporting in pmultiqc software table
+
+### `Removed`
+
+- [#702](https://github.com/bigbio/quantms/pull/702) **Remove DIA-NN workflow from quantms**: DIA users should use the dedicated repository [bigbio/quantmsdiann](https://github.com/bigbio/quantmsdiann)
+- [#701](https://github.com/bigbio/quantms/pull/701) **Remove MSstats post-processing step**: R scripts (`msstats_plfq.R`, `msstats_tmt.R`, `msstats_utils.R`) and corresponding modules removed. Users should run MSstats manually outside the pipeline.
+- [#706](https://github.com/bigbio/quantms/pull/706) Remove `ms2features_range` modes (`by_sample`, `by_project`) and IDRipper module. Only `independent_run` per-file Percolator is now supported.
+- [#708](https://github.com/bigbio/quantms/pull/708) Remove ConsensusID module; migrate to parquet-based processing
+
+### `Dependencies`
+
+- Updated quantms-utils to version 0.0.25
+- Updated quantms-rescoring (container permissions fix)
+- Migrated thermorawfileparser to bigbio/nf-modules
 
 ### `Deprecations`
 

conf/modules/id.config

@@ -6,16 +6,6 @@
 
 process {
 
-    // ID_SCORE_SWITCHER for phospho scoring
-    withName: '.*:ID:PHOSPHO_SCORING:ID_SCORE_SWITCHER' {
-        ext.args    = [
-            "-new_score_orientation lower_better",
-            "-old_score \"q-value\"",
-            "-new_score_type \"Posterior Error Probability\"",
-            "-debug $params.idscoreswitcher_debug"
-        ].join(' ').trim()
-    }
-
     // ONSITE phospho scoring
     withName: '.*:ID:PHOSPHO_SCORING:ONSITE' {
         ext.args    = "-debug $params.onsite_debug"
@@ -29,28 +19,6 @@ process {
         ].join(' ').trim()
     }
 
-    // EPIFANY
-    withName: '.*:PROTEIN_INFERENCE_EPIFANY' {
-        ext.args    = "-keep_best_psm_only false -debug $params.protein_inference_debug"
-    }
-
-    // PROTEIN_INFERENCE (generic)
-    withName: '.*:PROTEIN_INFERENCE' {
-        ext.args    = "-debug $params.protein_inference_debug"
-    }
-
-    // PSM FDR control ID_FILTER
-    withName: '.*:ID:PSM_FDR_CONTROL:ID_FILTER' {
-        ext.args    = "-score:psm \"$params.run_fdr_cutoff\""
-        ext.suffix  = '.idparquet'
-    }
-
-    // DDA_ID PSM FDR control ID_FILTER
-    withName: '.*:DDA_ID:PSM_FDR_CONTROL:ID_FILTER' {
-        ext.args    = "-score:psm \"$params.run_fdr_cutoff\""
-        ext.suffix  = '.idparquet'
-    }
-
     // MS2RESCORE
     withName: 'MSRESCORE_FEATURES' {
         ext.args   = [
@@ -60,13 +28,4 @@ process {
         ].join(' ').trim()
     }
 
-    // DDA_ID phospho scoring ID_SCORE_SWITCHER
-    withName: '.*:DDA_ID:PHOSPHO_SCORING:ID_SCORE_SWITCHER' {
-        ext.args   = [
-            "-new_score_orientation lower_better",
-            "-old_score \"q-value\"",
-            "-new_score_type \"Posterior Error Probability\"",
-            "-debug $params.idscoreswitcher_debug"
-        ].join(' ').trim()
-    }
 }

conf/modules/shared.config

@@ -42,15 +42,6 @@ process {
         ]
     }
 
-    // publishDir for all psm tables on id workflow
-    withName: '.*:PSM_CONVERSION' {
-        publishDir = [
-            path: { "${params.outdir}/psm_tables" },
-            mode: 'copy',
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     // publishDir for all features tables
     withName: '.*:MZML_STATISTICS' {
         publishDir = [

conf/modules/tmt.config

@@ -5,32 +5,6 @@
 */
 
 process {
-
-    // IDMAPPER
-    withName: '.*:TMT:.*:ID_MAPPER' {
-        ext.args    = "-debug $params.idmapper_debug"
-    }
-
-    // IDFILTER on PROTEIN LEVEL
-    withName: '.*:TMT:PROTEIN_INFERENCE:ID_FILTER' {
-        ext.args    = {
-            def level = params.protein_quant == 'strictly_unique_peptides' ? 'prot' : 'proteingroup'
-            def decoys_present = params.quantify_decoys ? ' ' : '-remove_decoys'
-            [
-                "-score:${level} \"$params.protein_level_fdr_cutoff\"",
-                "-score:psm \"$params.psm_level_fdr_cutoff\"",
-                "-delete_unreferenced_peptide_hits",
-                "${decoys_present}"
-            ].join(' ').trim()
-        }
-        ext.suffix  = '.consensusXML'
-    }
-
-    // PROTEINQUANTIFIER
-    withName: '.*:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER' {
-        ext.args    = "-debug $params.protein_quant_debug"
-    }
-
     // MSSTATSCONVERTER
     withName: '.*:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER' {
         ext.args    = "-debug $params.protein_quant_debug"

conf/modules/verbose_modules.config

@@ -124,38 +124,6 @@ process {
         ]
     }
 
-    withName: '.*:PROTEIN_INFERENCE_GENERIC|PROTEIN_INFERENCE_EPIFANY' {
-        publishDir = [
-            path: { "${params.outdir}/peptide_postprocessing/protein_inference" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*:FILE_MERGE' {
-        publishDir = [
-            path: { "${params.outdir}/peptide_postprocessing/file_merge" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*:ID_MAPPER' {
-        publishDir = [
-            path: { "${params.outdir}/peptide_postprocessing/id_mapper" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*:ID_SCORE_SWITCHER' {
-        publishDir = [
-            path: { "${params.outdir}/peptide_postprocessing/id_score_switcher" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     // Set the default publish for PTM processing steps
     withName: '.*:ONSITE' {
         publishDir = [
@@ -165,48 +133,6 @@ process {
         ]
     }
 
-    // DIANN preprocessing steps, final results will be stored in quant_tables directory
-    withName: '.*:INDIVIDUAL_ANALYSIS' {
-        publishDir = [
-            path: { "${params.outdir}/diann_preprocessing/individual_analysis" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*:PRELIMINARY_ANALYSIS' {
-        publishDir = [
-            path: { "${params.outdir}/diann_preprocessing/preliminary_analysis" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    // Database generation steps and subworkflows
-    withName: '.*:GENERATE_DECOY_DATABASE' {
-        publishDir = [
-            path: { "${params.outdir}/database_generation/generate_decoy_database" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*:ASSEMBLE_EMPIRICAL_LIBRARY' {
-        publishDir = [
-            path: { "${params.outdir}/database_generation/assemble_empirical_library" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: '.*:INSILICO_LIBRARY_GENERATION' {
-        publishDir = [
-            path: { "${params.outdir}/database_generation/insilico_library_generation" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: '.*:MSGF_DB_INDEXING' {
         publishDir = [
             path: { "${params.outdir}/database_generation/msgf_db_indexing" },
@@ -215,12 +141,4 @@ process {
         ]
     }
 
-    // Additional config files generated in DIANN configuration
-    withName: '.*:GENERATE_CFG' {
-        publishDir = [
-            path: { "${params.outdir}/sdrf" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
 }