bigbio · daichengxin · Jun 6, 2026 · Jun 6, 2026 · Jun 6, 2026 · Jun 6, 2026
diff --git a/AGENTS.md b/AGENTS.md
@@ -352,7 +352,7 @@ withName: 'OPENMS_PERCOLATORADAPTER' {
     publishDir = [
         path: { "${params.outdir}/intermediate_results/fdr_control" },
         mode: params.publish_dir_mode,
-        pattern: '*.idXML'
+        pattern: '*.idparquet'
     ]
 }
 ```

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -75,7 +75,7 @@ sp:
     fn: "*_ms_info.parquet"
     num_lines: 0
   pmultiqc/idXML:
-    fn: "*.idXML"
+    fn: "*.idparquet"
     num_lines: 0
   pmultiqc/msstats:
     fn: "*msstats_in.csv"

diff --git a/conf/modules/id.config b/conf/modules/id.config
@@ -6,11 +6,6 @@
 
 process {
 
-    // FDRCONSENSUSID
-    withName: '.*:FDR_CONSENSUSID' {
-        ext.args    = "-PSM true -protein false"
-    }
-
     // ID_SCORE_SWITCHER for phospho scoring
     withName: '.*:ID:PHOSPHO_SCORING:ID_SCORE_SWITCHER' {
         ext.args    = [
@@ -47,13 +42,13 @@ process {
     // PSM FDR control ID_FILTER
     withName: '.*:ID:PSM_FDR_CONTROL:ID_FILTER' {
         ext.args    = "-score:psm \"$params.run_fdr_cutoff\""
-        ext.suffix  = '.idXML'
+        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  = '.idXML'
+        ext.suffix  = '.idparquet'
     }
 
     // MS2RESCORE

diff --git a/conf/modules/shared.config b/conf/modules/shared.config
@@ -34,7 +34,7 @@ process {
     }
 
     // Result tables from multiple pipelines including LFQ, TMT, DDA
-    withName: '.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER' {
+    withName: '.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|ISOBARIC_WORKFLOW' {
         publishDir = [
             path: { "${params.outdir}/quant_tables" },
             mode: 'copy',

diff --git a/modules/local/openms/comet/meta.yml b/modules/local/openms/comet/meta.yml
@@ -29,7 +29,7 @@ output:
   - id_files_comet:
       type: file
       description: Output file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file

diff --git a/modules/local/openms/consensusid/main.nf b/modules/local/openms/consensusid/main.nf
diff --git a/modules/local/openms/consensusid/meta.yml b/modules/local/openms/consensusid/meta.yml
diff --git a/modules/local/openms/extractfeatures/main.nf b/modules/local/openms/extractfeatures/main.nf
@@ -36,4 +36,4 @@ process EXTRACTPSMFEATURES {
         PSMFeatureExtractor: \$(PSMFeatureExtractor 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
     END_VERSIONS
     """
-}
+}
diff --git a/...ocal/openms/false_discovery_rate/meta.yml → ...les/local/openms/extractfeatures/meta.yml b/...ocal/openms/false_discovery_rate/meta.yml → ...les/local/openms/extractfeatures/meta.yml
@@ -1,33 +1,34 @@
-name: false_discovery_rate
-description: Estimates the false discovery rate on peptide and protein level using decoy searches.
+name: EXTRACTPSMFEATURES
+description: Extracts PSM features from multiple search engines for rescoring.
 keywords:
-  - FDR
-  - decoy
+  - PSM
+  - feature extraction
+  - rescoring
   - OpenMS
 tools:
-  - FalseDiscoveryRate:
+  - PSMFeatureExtractor:
       description: |
-        Tool to estimate the false discovery rate on peptide and protein level.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_FalseDiscoveryRate.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_FalseDiscoveryRate.html
+        Tool to extract PSM features from identification results for downstream rescoring.
+      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_PSMFeatureExtractor.html
+      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_PSMFeatureExtractor.html
 input:
   - meta:
       type: map
       description: Groovy Map containing sample information
-  - id_file:
+  - id_files:
       type: file
       description: |
-        Identifications from searching a target-decoy database.
-      pattern: "*.idXML"
+        Identification files from one or multiple search engines.
+      pattern: "*.idparquet"
 output:
   - meta:
       type: map
       description: Groovy Map containing sample information
-  - id_files_idx_ForIDPEP_FDR:
+  - id_files_feat:
       type: file
       description: |
-        Identifications with annotated FDR.
-      pattern: "*.idXML"
+        PSM features in Parquet format for rescoring.
+      pattern: "*_feat.idparquet"
   - log:
       type: file
       description: log file

diff --git a/modules/local/openms/false_discovery_rate/main.nf b/modules/local/openms/false_discovery_rate/main.nf
diff --git a/modules/local/openms/id_conflict_resolver/main.nf b/modules/local/openms/id_conflict_resolver/main.nf
diff --git a/modules/local/openms/id_conflict_resolver/meta.yml b/modules/local/openms/id_conflict_resolver/meta.yml
diff --git a/modules/local/openms/id_filter/main.nf b/modules/local/openms/id_filter/main.nf
@@ -1,5 +1,5 @@
 process ID_FILTER {
-    tag {task.ext.suffix == ".idXML" ? "$meta.mzml_id" : "$id_file.baseName"}
+    tag {task.ext.suffix == ".idparquet" ? "$meta.mzml_id" : "$id_file.baseName"}
     label 'process_very_low'
     label 'process_single'
     label 'openms'

diff --git a/modules/local/openms/id_mapper/main.nf b/modules/local/openms/id_mapper/main.nf
diff --git a/modules/local/openms/id_mapper/meta.yml b/modules/local/openms/id_mapper/meta.yml
-Original file line number
+Diff line change
@@ Expand Up / @@ -36,4 +36,4 @@ process EXTRACTPSMFEATURES { @@
             PSMFeatureExtractor: \$(PSMFeatureExtractor 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
         END_VERSIONS
         """
-    }
+    }