From 0dccd6e4595730cb52bb93c0d2bcd8e132037a2e Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 11:23:41 +0800
Subject: [PATCH 01/12] remove consensusid and move to parquet

---
 modules/local/utils/psm_clean/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/utils/psm_clean/main.nf b/modules/local/utils/psm_clean/main.nf
index aa8fc3b4..201a85b4 100644
--- a/modules/local/utils/psm_clean/main.nf
+++ b/modules/local/utils/psm_clean/main.nf
@@ -25,9 +25,9 @@ process PSM_CLEAN {
     rescoring psm_feature_clean \\
         --idparquet $idparquet \\
         --mzml $mzml \\
-        --output ${idxml.baseName}_clean.idparquet \\
+        --output ${idparquet.baseName}_clean.idparquet \\
         $args \\
-        2>&1 | tee ${idxml.baseName}_clean.log
+        2>&1 | tee ${idparquet.baseName}_clean.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 59e94618acb10261deb1cd6fd4213af1ff2bc6e8 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 11:37:42 +0800
Subject: [PATCH 02/12] update

---
 AGENTS.md                                     |  2 +-
 assets/multiqc_config.yml                     |  2 +-
 conf/modules/id.config                        |  4 +-
 modules/local/openms/comet/meta.yml           |  2 +-
 modules/local/openms/consensusid/main.nf      | 40 -------------------
 modules/local/openms/consensusid/meta.yml     | 40 -------------------
 modules/local/openms/extractfeatures/main.nf  |  1 -
 .../meta.yml                                  | 29 +++++++-------
 .../local/openms/false_discovery_rate/main.nf | 40 -------------------
 modules/local/openms/id_filter/main.nf        |  2 +-
 .../local/openms/id_score_switcher/main.nf    |  4 +-
 .../local/openms/id_score_switcher/meta.yml   |  2 +-
 modules/local/openms/index_peptides/main.nf   |  4 +-
 modules/local/openms/index_peptides/meta.yml  |  4 +-
 modules/local/openms/msgf/meta.yml            |  2 +-
 modules/local/openms/percolator/meta.yml      |  2 +-
 modules/local/openms/proteomicslfq/main.nf    | 12 +++---
 modules/local/openms/proteomicslfq/meta.yml   |  2 +-
 modules/local/openms/sage/meta.yml            |  2 +-
 .../local/utils/msrescore_features/meta.yml   |  4 +-
 .../utils/msrescore_fine_tuning/meta.yml      |  4 +-
 modules/local/utils/psm_clean/meta.yml        |  4 +-
 modules/local/utils/psm_conversion/meta.yml   |  2 +-
 modules/local/utils/spectrum_features/main.nf |  6 +--
 .../local/utils/spectrum_features/meta.yml    |  4 +-
 .../local/peptide_database_search/main.nf     |  4 +-
 26 files changed, 52 insertions(+), 172 deletions(-)
 delete mode 100644 modules/local/openms/consensusid/main.nf
 delete mode 100644 modules/local/openms/consensusid/meta.yml
 rename modules/local/openms/{false_discovery_rate => extractfeatures}/meta.yml (51%)
 delete mode 100644 modules/local/openms/false_discovery_rate/main.nf

diff --git a/AGENTS.md b/AGENTS.md
index 453c8ac7..ebc18f2a 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -352,7 +352,7 @@ withName: 'OPENMS_PERCOLATORADAPTER' {
     publishDir = [
         path: { "${params.outdir}/intermediate_results/fdr_control" },
         mode: params.publish_dir_mode,
-        pattern: '*.idXML'
+        pattern: '*.idparquet'
     ]
 }
 ```
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 3a52d98a..40d716fd 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -75,7 +75,7 @@ sp:
     fn: "*_ms_info.parquet"
     num_lines: 0
   pmultiqc/idXML:
-    fn: "*.idXML"
+    fn: "*.idparquet"
     num_lines: 0
   pmultiqc/msstats:
     fn: "*msstats_in.csv"
diff --git a/conf/modules/id.config b/conf/modules/id.config
index 1b2a4ac4..8e26888c 100644
--- a/conf/modules/id.config
+++ b/conf/modules/id.config
@@ -47,13 +47,13 @@ process {
     // PSM FDR control ID_FILTER
     withName: '.*:ID:PSM_FDR_CONTROL:ID_FILTER' {
         ext.args    = "-score:psm \"$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/modules/local/openms/comet/meta.yml b/modules/local/openms/comet/meta.yml
index 5f255f4f..a36a020c 100644
--- 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
deleted file mode 100644
index 76346fb2..00000000
--- a/modules/local/openms/consensusid/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-process CONSENSUSID {
-    tag "$meta.mzml_id"
-    label 'process_single'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(id_file)
-
-    output:
-    tuple val(meta), path("${meta.mzml_id}_consensus.idXML"), emit: consensusids
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
-
-    """
-    ConsensusID \\
-        -in ${id_file} \\
-        -out ${meta.mzml_id}_consensus.idXML \\
-        -per_spectrum \\
-        -threads $task.cpus \\
-        -algorithm $params.consensusid_algorithm \\
-        -filter:min_support $params.min_consensus_support \\
-        -filter:considered_hits $params.consensusid_considered_top_hits \\
-        -debug $params.consensusid_debug \\
-        $args \\
-        2>&1 | tee ${meta.mzml_id}_consensusID.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ConsensusID: \$(ConsensusID 2>&1  | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/consensusid/meta.yml b/modules/local/openms/consensusid/meta.yml
deleted file mode 100644
index c8a7df5a..00000000
--- a/modules/local/openms/consensusid/meta.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: consensusid
-description: Computes a consensus from results of multiple peptide identification engines.
-keywords:
-  - consensus scoring
-  - peptide database search
-  - OpenMS
-tools:
-  - ConsensusID:
-      description: |
-        Tool to Computes a consensus from results of multiple peptide identification engines.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ConsensusID.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ConsensusID.html
-input:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - id_file:
-      type: file
-      description: |
-        Putative peptide-spectrum matches in idXML format (potentially multiple per spectrum). Score needs to be comparable (e.g. probability)
-      pattern: "*.idXML"
-output:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - id_files_idx_ForIDPEP_FDR:
-      type: file
-      description: |
-        Identifications with annotated FDR.
-      pattern: "*.idXML"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/extractfeatures/main.nf b/modules/local/openms/extractfeatures/main.nf
index 046921f8..f5ca9fa1 100644
--- a/modules/local/openms/extractfeatures/main.nf
+++ b/modules/local/openms/extractfeatures/main.nf
@@ -36,4 +36,3 @@ process EXTRACTPSMFEATURES {
         PSMFeatureExtractor: \$(PSMFeatureExtractor 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
     END_VERSIONS
     """
-}
\ No newline at end of file
diff --git a/modules/local/openms/false_discovery_rate/meta.yml b/modules/local/openms/extractfeatures/meta.yml
similarity index 51%
rename from modules/local/openms/false_discovery_rate/meta.yml
rename to modules/local/openms/extractfeatures/meta.yml
index 62fa100f..eff674af 100644
--- a/modules/local/openms/false_discovery_rate/meta.yml
+++ b/modules/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
deleted file mode 100644
index 37a872dd..00000000
--- a/modules/local/openms/false_discovery_rate/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-process FALSE_DISCOVERY_RATE {
-    tag "$meta.mzml_id"
-    label 'process_low'
-    label 'process_single'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(id_file)
-
-    output:
-    tuple val(meta), path("${id_file.baseName}_fdr.idXML"), emit: id_files_idx_ForIDPEP_FDR
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
-
-    """
-    FalseDiscoveryRate \\
-        -in ${id_file} \\
-        -out ${id_file.baseName}_fdr.idXML \\
-        -threads $task.cpus \\
-        -FDR:PSM ${params.run_fdr_cutoff} \\
-        -algorithm:add_decoy_peptides \\
-        -algorithm:add_decoy_proteins \\
-        -algorithm:conservative ${params.fdr_conservative} \\
-        $args \\
-        2>&1 | tee ${id_file.baseName}_fdr.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        FalseDiscoveryRate: \$(FalseDiscoveryRate 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/id_filter/main.nf b/modules/local/openms/id_filter/main.nf
index 0f939bf2..2bf6c8cf 100644
--- 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_score_switcher/main.nf b/modules/local/openms/id_score_switcher/main.nf
index bedd9fd7..97a9cd76 100644
--- a/modules/local/openms/id_score_switcher/main.nf
+++ b/modules/local/openms/id_score_switcher/main.nf
@@ -12,7 +12,7 @@ process ID_SCORE_SWITCHER {
     tuple val(meta), path(id_file), val(new_score)
 
     output:
-    tuple val(meta), path("${id_file.baseName}_pep.idXML"), emit: id_score_switcher
+    tuple val(meta), path("${id_file.baseName}_pep.idparquet"), emit: id_score_switcher
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
@@ -23,7 +23,7 @@ process ID_SCORE_SWITCHER {
     """
     IDScoreSwitcher \\
         -in ${id_file} \\
-        -out ${id_file.baseName}_pep.idXML \\
+        -out ${id_file.baseName}_pep.idparquet \\
         -threads $task.cpus \\
         -new_score ${new_score} \\
         $args \\
diff --git a/modules/local/openms/id_score_switcher/meta.yml b/modules/local/openms/id_score_switcher/meta.yml
index 246d603b..d20a3c52 100644
--- a/modules/local/openms/id_score_switcher/meta.yml
+++ b/modules/local/openms/id_score_switcher/meta.yml
@@ -18,7 +18,7 @@ input:
       type: file
       description: |
         Identifications from searching a target-decoy database.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
 output:
   - meta:
       type: map
diff --git a/modules/local/openms/index_peptides/main.nf b/modules/local/openms/index_peptides/main.nf
index e0628abb..6849853e 100644
--- a/modules/local/openms/index_peptides/main.nf
+++ b/modules/local/openms/index_peptides/main.nf
@@ -12,7 +12,7 @@ process INDEX_PEPTIDES {
 
 
     output:
-    tuple val(meta), path("${id_file.baseName}_idx.idXML"), emit: id_files_idx
+    tuple val(meta), path("${id_file.baseName}_idx.idparquet"), emit: id_files_idx
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
@@ -45,7 +45,7 @@ process INDEX_PEPTIDES {
     """
     PeptideIndexer \\
         -in ${id_file} \\
-        -out ${id_file.baseName}_idx.idXML \\
+        -out ${id_file.baseName}_idx.idparquet \\
         -threads $task.cpus \\
         -fasta ${database} \\
         -enzyme:name "${enzyme}" \\
diff --git a/modules/local/openms/index_peptides/meta.yml b/modules/local/openms/index_peptides/meta.yml
index eb937b22..2a784d7f 100644
--- a/modules/local/openms/index_peptides/meta.yml
+++ b/modules/local/openms/index_peptides/meta.yml
@@ -18,7 +18,7 @@ input:
       type: file
       description: |
         Input idXML file containing the identifications.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - database:
       type: file
       description: |
@@ -32,7 +32,7 @@ output:
       type: file
       description: |
         Output idXML file.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file
diff --git a/modules/local/openms/msgf/meta.yml b/modules/local/openms/msgf/meta.yml
index 8c7c8690..d8fe9bce 100644
--- a/modules/local/openms/msgf/meta.yml
+++ b/modules/local/openms/msgf/meta.yml
@@ -29,7 +29,7 @@ output:
   - id_files_msgf:
       type: file
       description: Output file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file
diff --git a/modules/local/openms/percolator/meta.yml b/modules/local/openms/percolator/meta.yml
index b7be826d..aad911da 100644
--- a/modules/local/openms/percolator/meta.yml
+++ b/modules/local/openms/percolator/meta.yml
@@ -17,7 +17,7 @@ input:
       type: file
       description: |
         Input idXML file containing the identifications.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
 output:
   - meta:
       type: map
diff --git a/modules/local/openms/proteomicslfq/main.nf b/modules/local/openms/proteomicslfq/main.nf
index 176b71ae..bb2216c0 100644
--- a/modules/local/openms/proteomicslfq/main.nf
+++ b/modules/local/openms/proteomicslfq/main.nf
@@ -18,12 +18,12 @@ process PROTEOMICSLFQ {
     path "${expdes.baseName}_qpx", emit: out_qpx
     path "${expdes.baseName}_openms.consensusXML", emit: out_consensusXML
     path "*msstats_in.csv", emit: out_msstats, optional: true
-    path "debug_mergedIDs.idXML", emit: debug_mergedIDs, optional: true
-    path "debug_mergedIDs_inference.idXML", emit: debug_mergedIDs_inference, optional: true
-    path "debug_mergedIDsGreedyResolved.idXML", emit: debug_mergedIDsGreedyResolved, optional: true
-    path "debug_mergedIDsGreedyResolvedFDR.idXML", emit: debug_mergedIDsGreedyResolvedFDR, optional: true
-    path "debug_mergedIDsGreedyResolvedFDRFiltered.idXML", emit: debug_mergedIDsGreedyResolvedFDRFiltered, optional: true
-    path "debug_mergedIDsFDRFilteredStrictlyUniqueResolved.idXML", emit: debug_mergedIDsFDRFilteredStrictlyUniqueResolved, optional: true
+    path "debug_mergedIDs.idparquet", emit: debug_mergedIDs, optional: true
+    path "debug_mergedIDs_inference.idparquet", emit: debug_mergedIDs_inference, optional: true
+    path "debug_mergedIDsGreedyResolved.idparquet", emit: debug_mergedIDsGreedyResolved, optional: true
+    path "debug_mergedIDsGreedyResolvedFDR.idparquet", emit: debug_mergedIDsGreedyResolvedFDR, optional: true
+    path "debug_mergedIDsGreedyResolvedFDRFiltered.idparquet", emit: debug_mergedIDsGreedyResolvedFDRFiltered, optional: true
+    path "debug_mergedIDsFDRFilteredStrictlyUniqueResolved.idparquet", emit: debug_mergedIDsFDRFilteredStrictlyUniqueResolved, optional: true
     path "*.log", emit: log
     path "versions.yml", emit: versions
 
diff --git a/modules/local/openms/proteomicslfq/meta.yml b/modules/local/openms/proteomicslfq/meta.yml
index b8b327e1..7ca50007 100644
--- a/modules/local/openms/proteomicslfq/meta.yml
+++ b/modules/local/openms/proteomicslfq/meta.yml
@@ -18,7 +18,7 @@ input:
   - id_files:
       type: file
       description: Identifications in idXML or mzIdentML format with posterior error probabilities as score type.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - expdes:
       type: file
       description: An experimental design file
diff --git a/modules/local/openms/sage/meta.yml b/modules/local/openms/sage/meta.yml
index 11eed615..49690e82 100644
--- a/modules/local/openms/sage/meta.yml
+++ b/modules/local/openms/sage/meta.yml
@@ -29,7 +29,7 @@ output:
   - id_files_sage:
       type: file
       description: Output file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file
diff --git a/modules/local/utils/msrescore_features/meta.yml b/modules/local/utils/msrescore_features/meta.yml
index 208da0e7..fe8162c1 100644
--- a/modules/local/utils/msrescore_features/meta.yml
+++ b/modules/local/utils/msrescore_features/meta.yml
@@ -13,7 +13,7 @@ input:
   - idxml_file:
       type: file
       description: idXML identification file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - mzml:
       type: file
       description: spectrum data file
@@ -25,7 +25,7 @@ output:
   - idxml:
       type: file
       description: idXML identification file after MS2 rescoring
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - version:
       type: file
       description: File containing software version
diff --git a/modules/local/utils/msrescore_fine_tuning/meta.yml b/modules/local/utils/msrescore_fine_tuning/meta.yml
index dd98ac3f..72fb9a60 100644
--- a/modules/local/utils/msrescore_fine_tuning/meta.yml
+++ b/modules/local/utils/msrescore_fine_tuning/meta.yml
@@ -18,7 +18,7 @@ input:
   - idxml_file:
       type: file
       description: idXML identification file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - mzml:
       type: file
       description: spectrum data file
@@ -30,7 +30,7 @@ output:
   - idxml:
       type: file
       description: idXML identification file after MS2 rescoring
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - version:
       type: file
       description: File containing software version
diff --git a/modules/local/utils/psm_clean/meta.yml b/modules/local/utils/psm_clean/meta.yml
index 84b1505b..32fb1c40 100644
--- a/modules/local/utils/psm_clean/meta.yml
+++ b/modules/local/utils/psm_clean/meta.yml
@@ -13,7 +13,7 @@ input:
   - idxml_file:
       type: file
       description: idXML identification file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - mzml:
       type: file
       description: spectrum data file
@@ -25,7 +25,7 @@ output:
   - idxml:
       type: file
       description: idXML identification file after postprocessing
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - version:
       type: file
       description: File containing software version
diff --git a/modules/local/utils/psm_conversion/meta.yml b/modules/local/utils/psm_conversion/meta.yml
index b3b3317f..86b6171d 100644
--- a/modules/local/utils/psm_conversion/meta.yml
+++ b/modules/local/utils/psm_conversion/meta.yml
@@ -13,7 +13,7 @@ input:
   - idxml_file:
       type: file
       description: idXML identification file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - spectrum_df:
       type: file
       description: spectrum data file
diff --git a/modules/local/utils/spectrum_features/main.nf b/modules/local/utils/spectrum_features/main.nf
index baaa989b..b0ee0cc6 100644
--- a/modules/local/utils/spectrum_features/main.nf
+++ b/modules/local/utils/spectrum_features/main.nf
@@ -10,7 +10,7 @@ process SPECTRUM_FEATURES {
     tuple val(meta), path(id_file), val(search_engine), path(ms_file)
 
     output:
-    tuple val(meta), path("${id_file.baseName}_snr.idXML"), val(search_engine), emit: id_files_snr
+    tuple val(meta), path("${id_file.baseName}_snr.idparquet"), val(search_engine), emit: id_files_snr
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
@@ -21,8 +21,8 @@ process SPECTRUM_FEATURES {
     """
     rescoring spectrum2feature \\
         --mzml "${ms_file}" \\
-        --idxml "${id_file}" \\
-        --output "${id_file.baseName}_snr.idXML" \\
+        --idparquet "${id_file}" \\
+        --output "${id_file.baseName}_snr.idparquet" \\
         $args \\
         2>&1 | tee "${id_file.baseName}_snr_feature.log"
 
diff --git a/modules/local/utils/spectrum_features/meta.yml b/modules/local/utils/spectrum_features/meta.yml
index 1c53ddf9..4cfb9b9d 100644
--- a/modules/local/utils/spectrum_features/meta.yml
+++ b/modules/local/utils/spectrum_features/meta.yml
@@ -22,7 +22,7 @@ input:
       type: file
       description: |
         Input idXML file containing the identifications.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
 output:
   - meta:
       type: map
@@ -31,7 +31,7 @@ output:
       type: file
       description: |
         Output file in idXML format
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file
diff --git a/subworkflows/local/peptide_database_search/main.nf b/subworkflows/local/peptide_database_search/main.nf
index e22ac32d..8423d00d 100644
--- a/subworkflows/local/peptide_database_search/main.nf
+++ b/subworkflows/local/peptide_database_search/main.nf
@@ -172,7 +172,7 @@ workflow PEPTIDE_DATABASE_SEARCH {
         } else {
             ch_id_files_out = ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage)
         }
-        
+
     } else if (params.psm_clean == true) {
         ch_id_files = ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage)
         PSM_CLEAN(ch_id_files.combine(ch_mzmls_search, by: 0))
@@ -185,4 +185,4 @@ workflow PEPTIDE_DATABASE_SEARCH {
     emit:
     ch_id_files_idx = ch_id_files_out
     versions        = ch_versions
-}
\ No newline at end of file
+}

From 3f76281719dac8ea8b77a15afe1965b64534441f Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 11:46:32 +0800
Subject: [PATCH 03/12] Update main.nf

---
 modules/local/openms/extractfeatures/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/local/openms/extractfeatures/main.nf b/modules/local/openms/extractfeatures/main.nf
index f5ca9fa1..16340ee1 100644
--- a/modules/local/openms/extractfeatures/main.nf
+++ b/modules/local/openms/extractfeatures/main.nf
@@ -36,3 +36,4 @@ process EXTRACTPSMFEATURES {
         PSMFeatureExtractor: \$(PSMFeatureExtractor 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
     END_VERSIONS
     """
+}

From 35668812e268dbe1e1d8be2ffcbb1ba1be6b719d Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 11:53:43 +0800
Subject: [PATCH 04/12] Update main.nf

---
 subworkflows/local/dda_id/main.nf | 59 ++-----------------------------
 1 file changed, 3 insertions(+), 56 deletions(-)

diff --git a/subworkflows/local/dda_id/main.nf b/subworkflows/local/dda_id/main.nf
index 29daeeba..a145297c 100644
--- a/subworkflows/local/dda_id/main.nf
+++ b/subworkflows/local/dda_id/main.nf
@@ -1,9 +1,7 @@
 //
 // MODULE: Local to the pipeline
 //
-include { MSRESCORE_FEATURES   } from '../../../modules/local/utils/msrescore_features/main'
 include { PERCOLATOR           } from '../../../modules/local/openms/percolator/main'
-include { EXTRACTPSMFEATURES           } from '../../../modules/local/openms/extractfeatures/main'
 include { PSM_CONVERSION       } from '../../../modules/local/utils/psm_conversion/main'
 include { PHOSPHO_SCORING      } from '../phospho_scoring/main'
 
@@ -41,62 +39,11 @@ workflow DDA_ID {
     //
     // SUBWORKFLOW: Rescoring
     //
-    if (params.search_engines.tokenize(",").unique().size() > 1) {
-        if (params.ms2features_enable == true) {
-        // Only add ms2_model_dir if it's actually set and not empty
-            // Handle cases where parameter might be empty string, null, boolean true, or whitespace
-            // When --ms2features_model_dir is passed with no value, Nextflow may set it to boolean true
-            if (params.ms2features_model_dir && params.ms2features_model_dir != true) {
-                ms2_model_dir = channel.from(file(params.ms2features_model_dir, checkIfExists: true))
-            } else {
-                // create a fake channel when don't specify model dir
-                ms2_model_dir = channel.from(file("pretrained_models"))
-            }
 
-            ch_id_files_feats.groupTuple(size: params.search_engines.tokenize(",").unique().size())
-                .combine(ch_mzmls_search, by: 0)
-                .combine(ms2_model_dir).set{ ch_id_rescoring }
+    PERCOLATOR(ch_id_files_feats)
+    ch_rescoring_results = PERCOLATOR.out.id_files_perc
+    ch_software_versions = ch_software_versions.mix(PERCOLATOR.out.versions)
 
-            MSRESCORE_FEATURES(ch_id_rescoring)
-            ch_software_versions = ch_software_versions.mix(MSRESCORE_FEATURES.out.versions)
-            ch_id_files_feats = MSRESCORE_FEATURES.out.idxml
-            ch_id_files_feats.map { v -> [v[0], v[1]] }.set {ch_perc_input}
-
-        } else{
-            EXTRACTPSMFEATURES(ch_id_files_feats.groupTuple(size: params.search_engines.tokenize(",").unique().size()))
-            ch_consensus_input = EXTRACTPSMFEATURES.out.id_files_feat
-            ch_perc_input = ch_consensus_input
-        }
-        PERCOLATOR(ch_perc_input)
-        ch_rescoring_results = PERCOLATOR.out.id_files_perc
-        ch_software_versions = ch_software_versions.mix(PERCOLATOR.out.versions)
-    } else {
-        if (params.ms2features_enable == true) {
-            // Only add ms2_model_dir if it's actually set and not empty
-            // Handle cases where parameter might be empty string, null, boolean true, or whitespace
-            // When --ms2features_model_dir is passed with no value, Nextflow may set it to boolean true
-            if (params.ms2features_model_dir && params.ms2features_model_dir != true) {
-                ms2_model_dir = channel.from(file(params.ms2features_model_dir, checkIfExists: true))
-            } else {
-                // create a fake channel when don't specify model dir
-                ms2_model_dir = channel.from(file("pretrained_models"))
-            }
-
-            ch_id_files_feats.groupTuple(size: params.search_engines.tokenize(",").unique().size())
-                .combine(ch_mzmls_search, by: 0)
-                .combine(ms2_model_dir).set{ ch_id_rescoring }
-
-            MSRESCORE_FEATURES(ch_id_rescoring)
-            ch_software_versions = ch_software_versions.mix(MSRESCORE_FEATURES.out.versions)
-            ch_id_files_feats = MSRESCORE_FEATURES.out.idxml
-            ch_id_files_feats.map { v -> [v[0], v[1]] }.set {ch_perc_input}
-        } else {
-            ch_perc_input = ch_id_files_feats
-        }
-        PERCOLATOR(ch_perc_input)
-        ch_software_versions = ch_software_versions.mix(PERCOLATOR.out.versions)
-        ch_rescoring_results = PERCOLATOR.out.id_files_perc
-    }
 
     PSM_FDR_CONTROL(ch_rescoring_results)
     ch_software_versions = ch_software_versions.mix(PSM_FDR_CONTROL.out.versions)

From acf43d282ec0c1efa45adf2a508afd4244b886f2 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 12:07:47 +0800
Subject: [PATCH 05/12] update

---
 modules/local/openms/id_mapper/main.nf            | 4 ++--
 modules/local/utils/msrescore_fine_tuning/main.nf | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/local/openms/id_mapper/main.nf b/modules/local/openms/id_mapper/main.nf
index 1c88cede..945a04d2 100644
--- a/modules/local/openms/id_mapper/main.nf
+++ b/modules/local/openms/id_mapper/main.nf
@@ -4,8 +4,8 @@ process ID_MAPPER {
     label 'openms'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
+        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:latest' :
+        'ghcr.io/bigbio/openms-tools-thirdparty:latest' }"
 
     input:
     tuple val(meta), path(id_file), path(map_file)
diff --git a/modules/local/utils/msrescore_fine_tuning/main.nf b/modules/local/utils/msrescore_fine_tuning/main.nf
index aa7ae59b..f7e4fa7f 100644
--- a/modules/local/utils/msrescore_fine_tuning/main.nf
+++ b/modules/local/utils/msrescore_fine_tuning/main.nf
@@ -7,7 +7,7 @@ process MSRESCORE_FINE_TUNING {
         'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"
 
     input:
-    tuple val(meta), path(idxml), path(mzml), val(groupkey), path(ms2_model_dir)
+    tuple val(meta), path(idparquet), path(mzml), val(groupkey), path(ms2_model_dir)
 
     output:
     tuple val(groupkey), path("retained_ms2.pth") , emit: model_weight
@@ -49,7 +49,7 @@ process MSRESCORE_FINE_TUNING {
 
     """
     rescoring transfer_learning \\
-        --idxml ./ \\
+        --idparquet ${idparquet.join(' --idparquet ')} \\
         --mzml ./ \\
         --save_model_dir ./ \\
         --ms2_tolerance $ms2_tolerance \\

From 3d233db72e9850ecefd660f62a77f7599c612f73 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 12:32:18 +0800
Subject: [PATCH 06/12] bump

---
 modules/local/utils/msrescore_features/main.nf    | 2 +-
 modules/local/utils/msrescore_fine_tuning/main.nf | 4 ++--
 modules/local/utils/psm_clean/main.nf             | 4 ++--
 modules/local/utils/spectrum_features/main.nf     | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/local/utils/msrescore_features/main.nf b/modules/local/utils/msrescore_features/main.nf
index 79b4244a..2e96d952 100644
--- a/modules/local/utils/msrescore_features/main.nf
+++ b/modules/local/utils/msrescore_features/main.nf
@@ -3,7 +3,7 @@ process MSRESCORE_FEATURES {
     label 'process_medium'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.17' :
         'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
 
     input:
diff --git a/modules/local/utils/msrescore_fine_tuning/main.nf b/modules/local/utils/msrescore_fine_tuning/main.nf
index f7e4fa7f..36db5182 100644
--- a/modules/local/utils/msrescore_fine_tuning/main.nf
+++ b/modules/local/utils/msrescore_fine_tuning/main.nf
@@ -3,8 +3,8 @@ process MSRESCORE_FINE_TUNING {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.17' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
 
     input:
     tuple val(meta), path(idparquet), path(mzml), val(groupkey), path(ms2_model_dir)
diff --git a/modules/local/utils/psm_clean/main.nf b/modules/local/utils/psm_clean/main.nf
index 201a85b4..cd7a9892 100644
--- a/modules/local/utils/psm_clean/main.nf
+++ b/modules/local/utils/psm_clean/main.nf
@@ -3,8 +3,8 @@ process PSM_CLEAN {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.17' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
 
     input:
     tuple val(meta), path(idparquet), path(mzml)
diff --git a/modules/local/utils/spectrum_features/main.nf b/modules/local/utils/spectrum_features/main.nf
index b0ee0cc6..dad64be0 100644
--- a/modules/local/utils/spectrum_features/main.nf
+++ b/modules/local/utils/spectrum_features/main.nf
@@ -3,8 +3,8 @@ process SPECTRUM_FEATURES {
     label 'process_low'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.17' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
 
     input:
     tuple val(meta), path(id_file), val(search_engine), path(ms_file)

From d451d980b0c3e697b5a05031c6e14bbde275c5cc Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 15:29:34 +0800
Subject: [PATCH 07/12] update

---
 conf/modules/id.config                        |  5 -----
 modules/local/utils/spectrum_features/main.nf |  4 ++--
 subworkflows/local/phospho_scoring/main.nf    | 11 ++---------
 3 files changed, 4 insertions(+), 16 deletions(-)

diff --git a/conf/modules/id.config b/conf/modules/id.config
index 8e26888c..96670030 100644
--- 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    = [
diff --git a/modules/local/utils/spectrum_features/main.nf b/modules/local/utils/spectrum_features/main.nf
index dad64be0..101b8f7c 100644
--- a/modules/local/utils/spectrum_features/main.nf
+++ b/modules/local/utils/spectrum_features/main.nf
@@ -7,10 +7,10 @@ process SPECTRUM_FEATURES {
         'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
 
     input:
-    tuple val(meta), path(id_file), val(search_engine), path(ms_file)
+    tuple val(meta), path(id_file), path(ms_file)
 
     output:
-    tuple val(meta), path("${id_file.baseName}_snr.idparquet"), val(search_engine), emit: id_files_snr
+    tuple val(meta), path("${id_file.baseName}_snr.idparquet"), emit: id_files_snr
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
diff --git a/subworkflows/local/phospho_scoring/main.nf b/subworkflows/local/phospho_scoring/main.nf
index 13d5a80c..a233c33c 100644
--- a/subworkflows/local/phospho_scoring/main.nf
+++ b/subworkflows/local/phospho_scoring/main.nf
@@ -12,16 +12,9 @@ workflow PHOSPHO_SCORING {
 
     main:
     ch_version = channel.empty()
-    if (params.search_engines.split(",").size() != 1){
-        ID_SCORE_SWITCHER(ch_id_files.combine(channel.value("\"Posterior Error Probability_score\"")))
-        ch_version = ch_version.mix(ID_SCORE_SWITCHER.out.versions)
-        ONSITE(ch_mzml_files.join(ID_SCORE_SWITCHER.out.id_score_switcher))
-        ch_version = ch_version.mix(ONSITE.out.versions)
-    } else{
-        ONSITE(ch_mzml_files.join(ch_id_files))
-        ch_version = ch_version.mix(ONSITE.out.versions)
-    }
 
+    ONSITE(ch_mzml_files.join(ch_id_files))
+    ch_version = ch_version.mix(ONSITE.out.versions)
 
 
     emit:

From e2839a8fc9303ffab64fb01f11e9c3256d73f5aa Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 16:46:10 +0800
Subject: [PATCH 08/12] update TMT

---
 conf/modules/shared.config                    |  2 +-
 .../local/openms/id_conflict_resolver/main.nf | 33 -------
 .../openms/id_conflict_resolver/meta.yml      | 31 -------
 modules/local/openms/id_mapper/main.nf        | 36 --------
 modules/local/openms/id_mapper/meta.yml       | 40 ---------
 .../local/openms/isobaric_analyzer/main.nf    | 79 -----------------
 .../local/openms/isobaric_analyzer/meta.yml   | 37 --------
 .../local/openms/isobaric_workflow/main.nf    | 88 +++++++++++++++++++
 .../local/openms/isobaric_workflow/meta.yml   | 42 +++++++++
 .../openms/protein_inference_epifany/main.nf  | 39 --------
 .../openms/protein_inference_epifany/meta.yml | 34 -------
 .../openms/protein_inference_generic/main.nf  | 44 ----------
 .../openms/protein_inference_generic/meta.yml | 34 -------
 subworkflows/local/feature_mapper/main.nf     | 26 ------
 subworkflows/local/feature_mapper/meta.yml    | 29 ------
 subworkflows/local/protein_inference/main.nf  | 40 ---------
 subworkflows/local/protein_inference/meta.yml | 30 -------
 subworkflows/local/protein_quant/main.nf      | 30 -------
 subworkflows/local/protein_quant/meta.yml     | 30 -------
 workflows/tmt.nf                              | 46 +++++-----
 20 files changed, 153 insertions(+), 617 deletions(-)
 delete mode 100644 modules/local/openms/id_conflict_resolver/main.nf
 delete mode 100644 modules/local/openms/id_conflict_resolver/meta.yml
 delete mode 100644 modules/local/openms/id_mapper/main.nf
 delete mode 100644 modules/local/openms/id_mapper/meta.yml
 delete mode 100644 modules/local/openms/isobaric_analyzer/main.nf
 delete mode 100644 modules/local/openms/isobaric_analyzer/meta.yml
 create mode 100644 modules/local/openms/isobaric_workflow/main.nf
 create mode 100644 modules/local/openms/isobaric_workflow/meta.yml
 delete mode 100644 modules/local/openms/protein_inference_epifany/main.nf
 delete mode 100644 modules/local/openms/protein_inference_epifany/meta.yml
 delete mode 100644 modules/local/openms/protein_inference_generic/main.nf
 delete mode 100644 modules/local/openms/protein_inference_generic/meta.yml
 delete mode 100644 subworkflows/local/feature_mapper/main.nf
 delete mode 100644 subworkflows/local/feature_mapper/meta.yml
 delete mode 100644 subworkflows/local/protein_inference/main.nf
 delete mode 100644 subworkflows/local/protein_inference/meta.yml
 delete mode 100644 subworkflows/local/protein_quant/main.nf
 delete mode 100644 subworkflows/local/protein_quant/meta.yml

diff --git a/conf/modules/shared.config b/conf/modules/shared.config
index c796635e..1a9ee7c4 100644
--- 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: { "${params.outdir}/quant_tables" },
             mode: 'copy',
diff --git a/modules/local/openms/id_conflict_resolver/main.nf b/modules/local/openms/id_conflict_resolver/main.nf
deleted file mode 100644
index d9b135af..00000000
--- a/modules/local/openms/id_conflict_resolver/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-process ID_CONFLICT_RESOLVER {
-    label 'process_low'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    path consus_file
-
-    output:
-    path "${consus_file.baseName}_resconf.consensusXML", emit: pro_resconf
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-
-    """
-    IDConflictResolver \\
-        -in ${consus_file} \\
-        -threads $task.cpus \\
-        -out ${consus_file.baseName}_resconf.consensusXML \\
-        $args \\
-        2>&1 | tee ${consus_file.baseName}_resconf.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        IDConflictResolver: \$(IDConflictResolver 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/id_conflict_resolver/meta.yml b/modules/local/openms/id_conflict_resolver/meta.yml
deleted file mode 100644
index 62db48b4..00000000
--- a/modules/local/openms/id_conflict_resolver/meta.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-name: id_conflict_resolver
-description: Resolves ambiguous annotations of features with peptide identifications.
-keywords:
-  - ambiguous
-  - OpenMS
-tools:
-  - IDConflictResolver:
-      description: |
-        Resolves ambiguous annotations of features with peptide identifications.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDConflictResolver.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDConflictResolver.html
-input:
-  - consus_file:
-      type: file
-      description: |
-        Input file (data annotated with identifications)
-      pattern: "*.{featureXML,consensusXML}"
-output:
-  - pro_resconf:
-      type: file
-      description: Output file (data with one peptide identification per feature)
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/id_mapper/main.nf b/modules/local/openms/id_mapper/main.nf
deleted file mode 100644
index 945a04d2..00000000
--- a/modules/local/openms/id_mapper/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-process ID_MAPPER {
-    tag "$meta.mzml_id"
-    label 'process_medium'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:latest' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:latest' }"
-
-    input:
-    tuple val(meta), path(id_file), path(map_file)
-
-    output:
-    path "${id_file.baseName}_map.consensusXML", emit: id_map
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
-
-    """
-    IDMapper \\
-        -id ${id_file} \\
-        -in ${map_file} \\
-        -threads $task.cpus \\
-        -out ${id_file.baseName}_map.consensusXML \\
-        $args \\
-        2>&1 | tee ${id_file.baseName}_map.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        IDMapper: \$(IDMapper 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/id_mapper/meta.yml b/modules/local/openms/id_mapper/meta.yml
deleted file mode 100644
index 67e9ed6d..00000000
--- a/modules/local/openms/id_mapper/meta.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: id_mapper
-description: Assigns protein/peptide identifications to features or consensus features.
-keywords:
-  - feature
-  - identification
-  - OpenMS
-tools:
-  - IDMapper:
-      description: |
-        Assigns protein/peptide identifications to features or consensus features.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDMapper.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDMapper.html
-input:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - id_file:
-      type: file
-      description: |
-        Identifications file
-      pattern: "*.{idXML, mzid}"
-  - map_file:
-      type: file
-      description: Feature map/consensus map file
-      pattern: "*.{featureXML, consensusXML, mzq}"
-output:
-  - id_map:
-      type: file
-      description: Output file
-      pattern: "*.{featureXML, consensusXML, mzq}"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/isobaric_analyzer/main.nf b/modules/local/openms/isobaric_analyzer/main.nf
deleted file mode 100644
index 6db8e587..00000000
--- a/modules/local/openms/isobaric_analyzer/main.nf
+++ /dev/null
@@ -1,79 +0,0 @@
-process ISOBARIC_ANALYZER {
-    tag "$meta.mzml_id"
-    label 'process_medium'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(mzml_file)
-
-    output:
-    tuple val(meta), path("${mzml_file.baseName}_iso.consensusXML"),  emit: id_files_consensusXML
-    path "versions.yml",   emit: versions
-    path "*.log",   emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
-
-    if (params.quant_activation_method == "HCD" || params.quant_activation_method == "HCID") diss_meth = "auto"
-    else if (params.quant_activation_method == "CID") diss_meth = "Collision-induced dissociation"
-    else if (params.quant_activation_method == "ETD") diss_meth = "Electron transfer dissociation"
-    else if (params.quant_activation_method == "ECD") diss_meth = "Electron capture dissociation"
-
-    def iso_normalization = params.iso_normalization ? "-quantification:normalization" : ""
-    def isotope_correction = params.isotope_correction ? "-quantification:isotope_correction true" : "-quantification:isotope_correction false"
-
-    // Check for isotope correction and load the correction matrix
-    if (params.isotope_correction) {
-        if (params.plex_corr_matrix_file == null) {
-            error("plex_corr_matrix_file is required when isotope_correction is enabled")
-        }
-
-        // Read the matrix file and format it into the command-line format
-        // Read the matrix file, skipping lines that start with '#' and process the matrix
-        def matrix_lines = new File(params.plex_corr_matrix_file).readLines()
-        .findAll { line -> !line.startsWith('#') && line.trim() } // Skip lines starting with '#' and empty lines
-        .drop(1) // Assuming the first non-comment line is a header
-        .collect { line ->
-            def values = line.split('/')
-            // Handle different labelling types
-            if (meta.labelling_type == 'tmt18plex' || meta.labelling_type == 'tmt16plex') {
-                return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}/${values[5]}/${values[6]}/${values[7]}/${values[8]}\""
-            } else {
-                return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}\""
-            }
-        }
-
-    // Join the matrix lines into a format for the C++ tool
-    def correction_matrix = matrix_lines.join(" ")
-
-    isotope_correction += " -${meta.labelling_type}:correction_matrix ${correction_matrix}"
-    }
-
-    """
-    IsobaricAnalyzer \\
-        -type ${meta.labelling_type} \\
-        -in ${mzml_file} \\
-        -threads ${task.cpus} \\
-        -extraction:select_activation "${diss_meth}" \\
-        -extraction:reporter_mass_shift ${params.reporter_mass_shift} \\
-        -extraction:min_reporter_intensity ${params.min_reporter_intensity} \\
-        -extraction:min_precursor_purity ${params.min_precursor_purity} \\
-        -extraction:precursor_isotope_deviation ${params.precursor_isotope_deviation} \\
-        ${iso_normalization} \\
-        -${meta.labelling_type}:reference_channel ${params.reference_channel} \\
-        ${isotope_correction} \\
-        -out ${mzml_file.baseName}_iso.consensusXML \\
-        ${args} \\
-        2>&1 | tee ${mzml_file.baseName}_isob.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        IsobaricAnalyzer: \$(IsobaricAnalyzer --version 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/isobaric_analyzer/meta.yml b/modules/local/openms/isobaric_analyzer/meta.yml
deleted file mode 100644
index faf4c4ae..00000000
--- a/modules/local/openms/isobaric_analyzer/meta.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-name: isobaric_analyzer
-description: Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
-keywords:
-  - peak
-  - OpenMS
-tools:
-  - IsobaricAnalyzer:
-      description: |
-        Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html
-input:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - mzml_file:
-      type: file
-      description: Input profile data file.
-      pattern: "*.mzML"
-output:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - iso_consensusXML:
-      type: file
-      description: Output consensusXML file with quantitative information
-      pattern: "*.consensusXML"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/isobaric_workflow/main.nf b/modules/local/openms/isobaric_workflow/main.nf
new file mode 100644
index 00000000..4cf2d1af
--- /dev/null
+++ b/modules/local/openms/isobaric_workflow/main.nf
@@ -0,0 +1,88 @@
+process ISOBARIC_WORKFLOW {
+    tag "${expdes.baseName}"
+    label 'process_high'
+    label 'openms'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:latest' :
+        'ghcr.io/bigbio/openms-tools-thirdparty:latest' }"
+
+    input:
+    val(labelling_type)
+    path(mzmls)
+    path(id_files)
+    path(expdes)
+
+    output:
+    path "${expdes.baseName}_openms.mzTab", emit: out_mztab
+    path "${expdes.baseName}_openms.consensusXML", emit: out_consensusXML
+    path "${expdes.baseName}_qpx", emit: out_qpx
+    path "*.log", emit: log
+    path "versions.yml", emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def extractBaseName = { filename ->
+        def name = filename.toString()
+        name = name.replaceAll(/\.mzML$/, '')
+
+        if (name.endsWith('.idparquet')) {
+            name = name.replaceAll(/\.idparquet$/, '')
+            name = name.replaceAll(/_(comet|msgf|sage|consensus)(_perc)?(_filter)?(_fdr)?$/, '')
+        }
+        return name
+    }
+
+    def mzml_sorted = mzmls.collect().sort{ a, b ->
+        extractBaseName(a.name) <=> extractBaseName(b.name)
+    }
+    def id_sorted = id_files.collect().sort{ a, b ->
+        extractBaseName(a.name) <=> extractBaseName(b.name)
+    }
+
+    // Build isotope correction matrix argument if enabled
+    def isotope_correction = ""
+    if (params.isotope_correction && params.plex_corr_matrix_file != null) {
+        def matrix_lines = new File(params.plex_corr_matrix_file).readLines()
+            .findAll { !it.startsWith('#') && it.trim() }
+            .drop(1)
+            .collect { line ->
+                def values = line.split('/')
+                if (labelling_type == 'tmt18plex' || labelling_type == 'tmt16plex') {
+                    return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}/${values[5]}/${values[6]}/${values[7]}/${values[8]}\""
+                } else {
+                    return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}\""
+                }
+            }
+        def correction_matrix = matrix_lines.join(" ")
+        isotope_correction = "-quantification:isotope_correction true -${labelling_type}:correction_matrix ${correction_matrix}"
+    }
+
+    """
+    IsobaricWorkflow \\
+        -threads ${task.cpus} \\
+        -in ${mzml_sorted.join(' ')} \\
+        -in_id ${id_sorted.join(' ')} \\
+        -exp_design ${expdes} \\
+        -type ${labelling_type} \\
+        -inference_method ${params.protein_inference_method} \\
+        -protein_quantification ${params.protein_quant} \\
+        -psmFDR ${params.psm_level_fdr_cutoff} \\
+        -proteinFDR ${params.protein_level_fdr_cutoff} \\
+        -picked_fdr ${params.picked_fdr} \\
+        -picked_decoy_string ${params.decoy_string} \\
+        -extraction:min_precursor_purity ${params.min_precursor_purity} \\
+        -extraction:precursor_isotope_deviation ${params.precursor_isotope_deviation} \\
+        -extraction:min_reporter_intensity ${params.min_reporter_intensity} \\
+        ${isotope_correction} \\
+        -out ${expdes.baseName}_openms.consensusXML \\
+        -out_mzTab ${expdes.baseName}_openms.mzTab \\
+        -out_qpx ${expdes.baseName}_qpx \\
+        $args \\
+        2>&1 | tee isobaricworkflow.log
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        IsobaricWorkflow: \$(IsobaricWorkflow 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
+    END_VERSIONS
+    """
+}
\ No newline at end of file
diff --git a/modules/local/openms/isobaric_workflow/meta.yml b/modules/local/openms/isobaric_workflow/meta.yml
new file mode 100644
index 00000000..45971764
--- /dev/null
+++ b/modules/local/openms/isobaric_workflow/meta.yml
@@ -0,0 +1,42 @@
+name: isobaric_workflow
+description: Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
+keywords:
+  - OpenMS
+  - quantification
+tools:
+  - IsobaricWorkflow:
+      description: |
+        Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
+      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_IsobaricWorkflow.html
+      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_IsobaricWorkflow.html
+  - mzmls:
+      type: file
+      description: Input Spectra in mzML format
+      pattern: "*.mzML"
+  - id_files:
+      type: file
+      description: Identifications in idparquet or mzIdentML format with posterior error probabilities as score type.
+      pattern: "*.idparquet"
+  - expdes:
+      type: file
+      description: An experimental design file
+      pattern: "*.tsv"
+output:
+  - out_mztab:
+      type: file
+      description: mzTab file with analysis results
+      pattern: "*.mzTab"
+  - out_consensusXML:
+      type: file
+      description: ConsensusXML file for visualization and further processing in OpenMS.
+      pattern: "*.consensusXML"
+  - log:
+      type: file
+      description: log file
+      pattern: "*.log"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "versions.yml"
+authors:
+  - "@MaLLLiYA"
diff --git a/modules/local/openms/protein_inference_epifany/main.nf b/modules/local/openms/protein_inference_epifany/main.nf
deleted file mode 100644
index ddafba50..00000000
--- a/modules/local/openms/protein_inference_epifany/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-process PROTEIN_INFERENCE_EPIFANY {
-    label 'process_medium'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(consus_file)
-
-    output:
-    tuple val(meta), path("${consus_file.baseName}_epi.consensusXML"), emit: epi_inference
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    gg = params.protein_quant == 'shared_peptides' ? 'remove_proteins_wo_evidence' : 'none'
-
-    """
-    Epifany \\
-        -in ${consus_file} \\
-        -protein_fdr true \\
-        -threads $task.cpus \\
-        -algorithm:keep_best_PSM_only $params.keep_best_PSM_only \\
-        -algorithm:update_PSM_probabilities $params.update_PSM_probabilities \\
-        -greedy_group_resolution $gg \\
-        -algorithm:top_PSMs $params.top_PSMs \\
-        -out ${consus_file.baseName}_epi.consensusXML \\
-        $args \\
-        2>&1 | tee ${consus_file.baseName}_inference.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        Epifany: \$(Epifany 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/protein_inference_epifany/meta.yml b/modules/local/openms/protein_inference_epifany/meta.yml
deleted file mode 100644
index 23d09813..00000000
--- a/modules/local/openms/protein_inference_epifany/meta.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: protein_inference_epifany
-description: Runs a Bayesian protein inference.
-keywords:
-  - Bayesian
-  - inference
-  - OpenMS
-tools:
-  - Epifany:
-      description: |
-        It is a protein inference engine based on a Bayesian network.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_Epifany.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_Epifany.html
-input:
-  - consus_file:
-      type: file
-      description: |
-        identification results.
-      pattern: "*.{idXML,consensusXML}"
-output:
-  - epi_inference:
-      type: file
-      description: |
-        identification results with scored/grouped proteins.
-      pattern: "*.{idXML,consensusXML}"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/protein_inference_generic/main.nf b/modules/local/openms/protein_inference_generic/main.nf
deleted file mode 100644
index 8222fb63..00000000
--- a/modules/local/openms/protein_inference_generic/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-process PROTEIN_INFERENCE_GENERIC {
-    label 'process_medium'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(consus_file)
-
-    output:
-    tuple val(meta), path("${consus_file.baseName}_epi.consensusXML"), emit: protein_inference
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    gg = params.protein_quant == 'shared_peptides' ? '-Algorithm:greedy_group_resolution' : ''
-    groups = params.protein_quant == 'strictly_unique_peptides' ? 'false' : 'true'
-
-    """
-    ProteinInference \\
-        -in ${consus_file} \\
-        -threads $task.cpus \\
-        -picked_fdr $params.picked_fdr \\
-        -picked_decoy_string $params.decoy_string \\
-        -protein_fdr true \\
-        -Algorithm:use_shared_peptides $params.use_shared_peptides \\
-        -Algorithm:annotate_indistinguishable_groups $groups \\
-        -Algorithm:score_type "PEP" \\
-        $gg \\
-        -Algorithm:score_aggregation_method $params.protein_score \\
-        -Algorithm:min_peptides_per_protein $params.min_peptides_per_protein \\
-        -out ${consus_file.baseName}_epi.consensusXML \\
-        $args \\
-        2>&1 | tee ${consus_file.baseName}_inference.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ProteinInference: \$(ProteinInference 2>&1 | grep -E '^Version(.*) ' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/protein_inference_generic/meta.yml b/modules/local/openms/protein_inference_generic/meta.yml
deleted file mode 100644
index 98347934..00000000
--- a/modules/local/openms/protein_inference_generic/meta.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: protein_inference_generic
-description: Computes a protein identification score based on an aggregation of scores of identified peptides.
-keywords:
-  - protein
-  - inference
-  - OpenMS
-tools:
-  - ProteinInference:
-      description: |
-        Computes a protein identification score based on an aggregation of scores of identified peptides.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinInference.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinInference.html
-input:
-  - consus_file:
-      type: file
-      description: |
-        identification results.
-      pattern: "*.{idXML,consensusXML}"
-output:
-  - protein_inference:
-      type: file
-      description: |
-        identification results with scored/grouped proteins.
-      pattern: "*.consensusXML"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/subworkflows/local/feature_mapper/main.nf b/subworkflows/local/feature_mapper/main.nf
deleted file mode 100644
index 308293da..00000000
--- a/subworkflows/local/feature_mapper/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-//
-// Assigns protein/peptide identifications to features or consensus features.
-//
-
-include { ISOBARIC_ANALYZER } from '../../../modules/local/openms/isobaric_analyzer/main'
-include { ID_MAPPER         } from '../../../modules/local/openms/id_mapper/main'
-
-workflow FEATURE_MAPPER {
-    take:
-    ch_mzml_files
-    ch_id_files
-
-    main:
-    ch_version = channel.empty()
-
-    ISOBARIC_ANALYZER(ch_mzml_files)
-    ch_version = ch_version.mix(ISOBARIC_ANALYZER.out.versions)
-
-    ID_MAPPER(ch_id_files.combine(ISOBARIC_ANALYZER.out.id_files_consensusXML, by: 0))
-    ch_version = ch_version.mix(ID_MAPPER.out.versions)
-
-    emit:
-    id_map  = ID_MAPPER.out.id_map
-
-    versions = ch_version
-}
diff --git a/subworkflows/local/feature_mapper/meta.yml b/subworkflows/local/feature_mapper/meta.yml
deleted file mode 100644
index e2c40d97..00000000
--- a/subworkflows/local/feature_mapper/meta.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "feature_mapper"
-description: Subworkflow for mapping features across different runs and conditions
-keywords:
-  - feature
-  - mapping
-  - alignment
-  - proteomics
-components:
-  - isobaric/analyzer
-  - id/mapper
-input:
-  - ch_input:
-      type: file
-      description: |
-        Channel containing input files for feature mapping
-output:
-  - ch_mapped_features:
-      type: file
-      description: |
-        Channel containing mapped features
-  - versions:
-      type: file
-      description: |
-        Software versions used in this subworkflow
-authors:
-  - "@bigbio"
-maintainers:
-  - "@bigbio"
diff --git a/subworkflows/local/protein_inference/main.nf b/subworkflows/local/protein_inference/main.nf
deleted file mode 100644
index 96381089..00000000
--- a/subworkflows/local/protein_inference/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-//
-// ProteinInference
-//
-
-include { PROTEIN_INFERENCE_EPIFANY } from '../../../modules/local/openms/protein_inference_epifany/main'
-include { PROTEIN_INFERENCE_GENERIC } from '../../../modules/local/openms/protein_inference_generic/main'
-include { ID_FILTER                 } from '../../../modules/local/openms/id_filter/main'
-
-workflow PROTEIN_INFERENCE {
-    take:
-    ch_consus_file
-
-    main:
-    ch_version = channel.empty()
-
-    if (params.protein_inference_method == "bayesian") {
-        PROTEIN_INFERENCE_EPIFANY(ch_consus_file)
-        ch_version = ch_version.mix(PROTEIN_INFERENCE_EPIFANY.out.versions)
-        ch_inference = PROTEIN_INFERENCE_EPIFANY.out.epi_inference
-    } else {
-        PROTEIN_INFERENCE_GENERIC(ch_consus_file)
-        ch_version = ch_version.mix(PROTEIN_INFERENCE_GENERIC.out.versions)
-        ch_inference = PROTEIN_INFERENCE_GENERIC.out.protein_inference
-    }
-
-    ID_FILTER(ch_inference.combine(channel.value("-score:type_protein q-value")))
-    ch_version = ch_version.mix(ID_FILTER.out.versions)
-    ID_FILTER.out.id_filtered
-        .multiMap{ it ->
-            meta: it[0]
-            results: it[1]
-            }
-        .set{ ch_epi_results }
-
-    emit:
-    epi_idfilter    = ch_epi_results.results
-
-    versions         = ch_version
-
-}
diff --git a/subworkflows/local/protein_inference/meta.yml b/subworkflows/local/protein_inference/meta.yml
deleted file mode 100644
index 7bab69e8..00000000
--- a/subworkflows/local/protein_inference/meta.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "protein_inference"
-description: Subworkflow for protein inference from peptide identifications
-keywords:
-  - protein
-  - inference
-  - proteomics
-  - peptides
-components:
-  - protein/inference/epifany
-  - protein/inference/generic
-  - id/filter
-input:
-  - ch_input:
-      type: file
-      description: |
-        Channel containing input files for protein inference
-output:
-  - ch_protein_results:
-      type: file
-      description: |
-        Channel containing protein inference results
-  - versions:
-      type: file
-      description: |
-        Software versions used in this subworkflow
-authors:
-  - "@bigbio"
-maintainers:
-  - "@bigbio"
diff --git a/subworkflows/local/protein_quant/main.nf b/subworkflows/local/protein_quant/main.nf
deleted file mode 100644
index 6c9f295b..00000000
--- a/subworkflows/local/protein_quant/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-//
-// ProteinQuant
-//
-
-include { ID_CONFLICT_RESOLVER as ID_CONFLICT_RESOLVER } from '../../../modules/local/openms/id_conflict_resolver/main'
-include { PROTEIN_QUANTIFIER as PROTEIN_QUANTIFIER  } from '../../../modules/local/openms/protein_quantifier/main'
-include { MSSTATS_CONVERTER as MSSTATS_CONVERTER   } from '../../../modules/local/openms/msstats_converter/main'
-
-workflow PROTEIN_QUANT {
-    take:
-    ch_conflict_file
-    ch_expdesign_file
-
-    main:
-    ch_version = channel.empty()
-
-    ID_CONFLICT_RESOLVER(ch_conflict_file)
-    ch_version = ch_version.mix(ID_CONFLICT_RESOLVER.out.versions)
-
-    PROTEIN_QUANTIFIER(ID_CONFLICT_RESOLVER.out.pro_resconf, ch_expdesign_file)
-    ch_version = ch_version.mix(PROTEIN_QUANTIFIER.out.versions)
-
-    MSSTATS_CONVERTER(ID_CONFLICT_RESOLVER.out.pro_resconf, ch_expdesign_file, "ISO")
-    ch_version = ch_version.mix(MSSTATS_CONVERTER.out.versions)
-
-    emit:
-    msstats_csv = MSSTATS_CONVERTER.out.out_msstats
-    out_mztab   = PROTEIN_QUANTIFIER.out.out_mztab
-    versions = ch_version
-}
diff --git a/subworkflows/local/protein_quant/meta.yml b/subworkflows/local/protein_quant/meta.yml
deleted file mode 100644
index 71ae589f..00000000
--- a/subworkflows/local/protein_quant/meta.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "protein_quant"
-description: Subworkflow for protein quantification from MS data
-keywords:
-  - protein
-  - quantification
-  - proteomics
-  - ms
-components:
-  - id/conflict/resolver
-  - protein/quantifier
-  - msstats/converter
-input:
-  - ch_input:
-      type: file
-      description: |
-        Channel containing input files for protein quantification
-output:
-  - ch_quant_results:
-      type: file
-      description: |
-        Channel containing protein quantification results
-  - versions:
-      type: file
-      description: |
-        Software versions used in this subworkflow
-authors:
-  - "@bigbio"
-maintainers:
-  - "@bigbio"
diff --git a/workflows/tmt.nf b/workflows/tmt.nf
index 6a882cef..a8b9f0d6 100644
--- a/workflows/tmt.nf
+++ b/workflows/tmt.nf
@@ -7,14 +7,12 @@
 //
 // MODULES: Local to the pipeline
 //
-include { FILE_MERGE  } from '../modules/local/openms/file_merge/main'
+include { ISOBARIC_WORKFLOW } from '../modules/local/openms/isobaric_workflow/main'
+include { MSSTATS_CONVERTER } from '../modules/local/openms/msstats_converter/main'
 
 //
 // SUBWORKFLOWS: Consisting of a mix of local and nf-core/modules
 //
-include { FEATURE_MAPPER    } from '../subworkflows/local/feature_mapper/main'
-include { PROTEIN_INFERENCE } from '../subworkflows/local/protein_inference/main'
-include { PROTEIN_QUANT     } from '../subworkflows/local/protein_quant/main'
 include { ID                } from '../subworkflows/local/id/main'
 
 /*
@@ -40,28 +38,28 @@ workflow TMT {
     ch_software_versions = ch_software_versions.mix(ID.out.versions)
 
     //
-    // SUBWORKFLOW: FEATUREMAPPER
+    // SUBWORKFLOW: ISOBARIC_WORKFLOW
     //
-    FEATURE_MAPPER(ch_file_preparation_results, ID.out.id_results)
-    ch_software_versions = ch_software_versions.mix(FEATURE_MAPPER.out.versions)
+    // Extract labelling_type from meta (auto-detected from SDRF)
+    ch_file_preparation_results.join(ID.out.id_results)
+        .multiMap { it ->
+            labelling_type: it[0].labelling_type
+            mzmls: it[1]
+            ids: it[2]
+        }
+        .set{ ch_iso_workflow }
+    ISOBARIC_WORKFLOW(ch_iso_workflow.labelling_type.first(),
+                ch_iso_workflow.mzmls.collect(),
+                ch_iso_workflow.ids.collect(),
+                ch_expdesign
+            )
+    ch_software_versions = ch_software_versions.mix(ISOBARIC_WORKFLOW.out.versions)
 
     //
-    // MODULE: FILEMERGE
+    // SUBWORKFLOW: MSSTATS_CONVERTER
     //
-    FILE_MERGE(FEATURE_MAPPER.out.id_map.collect())
-    ch_software_versions = ch_software_versions.mix(FILE_MERGE.out.versions)
-
-    //
-    // SUBWORKFLOW: PROTEININFERENCE
-    //
-    PROTEIN_INFERENCE(FILE_MERGE.out.id_merge)
-    ch_software_versions = ch_software_versions.mix(PROTEIN_INFERENCE.out.versions)
-
-    //
-    // SUBWORKFLOW: PROTEINQUANT
-    //
-    PROTEIN_QUANT(PROTEIN_INFERENCE.out.epi_idfilter, ch_expdesign)
-    ch_software_versions = ch_software_versions.mix(PROTEIN_QUANT.out.versions)
+    MSSTATS_CONVERTER(ISOBARIC_WORKFLOW.out.out_consensusXML, ch_expdesign, "ISO")
+    ch_software_versions = ch_software_versions.mix(MSSTATS_CONVERTER.out.versions)
 
     ID.out.psmrescoring_results
         .map { it -> it[1] }
@@ -74,7 +72,7 @@ workflow TMT {
     emit:
     ch_pmultiqc_ids         = ch_pmultiqc_ids
     ch_pmultiqc_consensus   = ch_pmultiqc_consensus
-    final_result            = PROTEIN_QUANT.out.out_mztab
-    msstats_in              = PROTEIN_QUANT.out.msstats_csv
+    final_result            = ISOBARIC_WORKFLOW.out.out_mztab
+    msstats_in              = MSSTATS_CONVERTER.out.out_msstats
     versions                = ch_software_versions
 }

From 2f6e1c5d77571b6f4900ca01c1a8fd12f87790a1 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 16:48:06 +0800
Subject: [PATCH 09/12] Update main.nf

---
 modules/local/openms/isobaric_workflow/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/openms/isobaric_workflow/main.nf b/modules/local/openms/isobaric_workflow/main.nf
index 4cf2d1af..f335c7d0 100644
--- a/modules/local/openms/isobaric_workflow/main.nf
+++ b/modules/local/openms/isobaric_workflow/main.nf
@@ -85,4 +85,4 @@ process ISOBARIC_WORKFLOW {
         IsobaricWorkflow: \$(IsobaricWorkflow 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
     END_VERSIONS
     """
-}
\ No newline at end of file
+}

From 1edb72a00c693c31b9d81232b11703dd8cfb3eca Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sat, 6 Jun 2026 16:55:59 +0800
Subject: [PATCH 10/12] Update main.nf

---
 .../local/openms/isobaric_workflow/main.nf    | 21 ++-----------------
 1 file changed, 2 insertions(+), 19 deletions(-)

diff --git a/modules/local/openms/isobaric_workflow/main.nf b/modules/local/openms/isobaric_workflow/main.nf
index f335c7d0..8a2e5418 100644
--- a/modules/local/openms/isobaric_workflow/main.nf
+++ b/modules/local/openms/isobaric_workflow/main.nf
@@ -22,23 +22,6 @@ process ISOBARIC_WORKFLOW {
 
     script:
     def args = task.ext.args ?: ''
-    def extractBaseName = { filename ->
-        def name = filename.toString()
-        name = name.replaceAll(/\.mzML$/, '')
-
-        if (name.endsWith('.idparquet')) {
-            name = name.replaceAll(/\.idparquet$/, '')
-            name = name.replaceAll(/_(comet|msgf|sage|consensus)(_perc)?(_filter)?(_fdr)?$/, '')
-        }
-        return name
-    }
-
-    def mzml_sorted = mzmls.collect().sort{ a, b ->
-        extractBaseName(a.name) <=> extractBaseName(b.name)
-    }
-    def id_sorted = id_files.collect().sort{ a, b ->
-        extractBaseName(a.name) <=> extractBaseName(b.name)
-    }
 
     // Build isotope correction matrix argument if enabled
     def isotope_correction = ""
@@ -61,8 +44,8 @@ process ISOBARIC_WORKFLOW {
     """
     IsobaricWorkflow \\
         -threads ${task.cpus} \\
-        -in ${mzml_sorted.join(' ')} \\
-        -in_id ${id_sorted.join(' ')} \\
+        -in ${mzmls.join(' ')} \\
+        -in_id ${id_files.join(' ')} \\
         -exp_design ${expdes} \\
         -type ${labelling_type} \\
         -inference_method ${params.protein_inference_method} \\

From 82d2f5d228af0779ca2d9984d5191140dbe34511 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Tue, 9 Jun 2026 13:13:08 +0800
Subject: [PATCH 11/12] update

---
 .../local/utils/msrescore_fine_tuning/main.nf | 14 ++---
 modules/local/utils/psm_clean/main.nf         |  6 +-
 .../local/peptide_database_search/main.nf     | 56 +++++--------------
 3 files changed, 24 insertions(+), 52 deletions(-)

diff --git a/modules/local/utils/msrescore_fine_tuning/main.nf b/modules/local/utils/msrescore_fine_tuning/main.nf
index 36db5182..75a5b5a3 100644
--- a/modules/local/utils/msrescore_fine_tuning/main.nf
+++ b/modules/local/utils/msrescore_fine_tuning/main.nf
@@ -7,19 +7,19 @@ process MSRESCORE_FINE_TUNING {
         'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
 
     input:
-    tuple val(meta), path(idparquet), path(mzml), val(groupkey), path(ms2_model_dir)
+    tuple val(meta), path(idparquet), path(mzml), path(ms2_model_dir)
 
     output:
-    tuple val(groupkey), path("retained_ms2.pth") , emit: model_weight
-    path "versions.yml"                           , emit: versions
-    path "*.log"                                  , emit: log
+    path("retained_ms2.pth") , emit: model_weight
+    path "versions.yml"      , emit: versions
+    path "*.log"             , emit: log
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${groupkey}_fine_tuning"
+    def prefix = task.ext.prefix ?: "fine_tuning"
 
     // Initialize tolerance variables
     def ms2_tolerance = null
@@ -50,7 +50,7 @@ process MSRESCORE_FINE_TUNING {
     """
     rescoring transfer_learning \\
         --idparquet ${idparquet.join(' --idparquet ')} \\
-        --mzml ./ \\
+        --mzml ${mzml.join(' --mzml ')} \\
         --save_model_dir ./ \\
         --ms2_tolerance $ms2_tolerance \\
         --ms2_tolerance_unit $ms2_tolerance_unit \\
@@ -62,7 +62,7 @@ process MSRESCORE_FINE_TUNING {
         ${force_transfer_learning} \\
         ${consider_modloss} \\
         $args \\
-        2>&1 | tee ${groupkey}_fine_tuning.log
+        2>&1 | tee fine_tuning.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/utils/psm_clean/main.nf b/modules/local/utils/psm_clean/main.nf
index cd7a9892..a132e146 100644
--- a/modules/local/utils/psm_clean/main.nf
+++ b/modules/local/utils/psm_clean/main.nf
@@ -23,11 +23,11 @@ process PSM_CLEAN {
 
     """
     rescoring psm_feature_clean \\
-        --idparquet $idparquet \\
+        --idparquet ${idparquet.join(' --idparquet ')} \\
         --mzml $mzml \\
-        --output ${idparquet.baseName}_clean.idparquet \\
+        --output ${mzml.baseName}_clean.idparquet \\
         $args \\
-        2>&1 | tee ${idparquet.baseName}_clean.log
+        2>&1 | tee ${mzml.baseName}_clean.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/subworkflows/local/peptide_database_search/main.nf b/subworkflows/local/peptide_database_search/main.nf
index 8423d00d..fd94db2d 100644
--- a/subworkflows/local/peptide_database_search/main.nf
+++ b/subworkflows/local/peptide_database_search/main.nf
@@ -91,57 +91,29 @@ workflow PEPTIDE_DATABASE_SEARCH {
                 } else {
 
                     // Preparing train datasets and fine tuning MS2 model
-                    sage_train_datasets = ch_id_sage
+                    train_datasets = ch_id_sage.mix(ch_id_msgf).mix(ch_id_comet)
                         .combine(ch_mzmls_search, by: 0)
                         .toSortedList()
                         .flatMap()
                         .randomSample(params.fine_tuning_sample_run, 2025)
-                        .combine(channel.value("sage"))
                         .groupTuple(by: 3)
 
-                    msgf_train_datasets = ch_id_msgf
-                        .combine(ch_mzmls_search, by: 0)
-                        .toSortedList()
-                        .flatMap()
-                        .randomSample(params.fine_tuning_sample_run, 2025)
-                        .combine(channel.value("msgf"))
-                        .groupTuple(by: 3)
-
-                    comet_train_datasets = ch_id_comet
-                        .combine(ch_mzmls_search, by: 0)
-                        .toSortedList()
-                        .flatMap()
-                        .randomSample(params.fine_tuning_sample_run, 2025)
-                        .combine(channel.value("comet"))
-                        .groupTuple(by: 3)
-
-                    sage_train_datasets.mix(msgf_train_datasets)
-                        .mix(comet_train_datasets)
-                        .combine(ms2_model_dir)
-                        .set { train_datasets }
-                    MSRESCORE_FINE_TUNING(train_datasets)
+                    MSRESCORE_FINE_TUNING(train_datasets.combine(ms2_model_dir))
                     ch_versions = ch_versions.mix(MSRESCORE_FINE_TUNING.out.versions)
 
-                    channel.value("msgf").combine(ch_id_msgf.combine(ch_mzmls_search, by: 0))
-                        .combine(MSRESCORE_FINE_TUNING.out.model_weight, by:0)
-                        .map { v -> [v[1], v[2], v[3], v[4], v[0] ] }
-                        .set { msgf_features_input }
-
-                    channel.value("sage").combine(ch_id_sage.combine(ch_mzmls_search, by: 0))
-                        .combine(MSRESCORE_FINE_TUNING.out.model_weight, by:0)
-                        .map { v -> [v[1], v[2], v[3], v[4], v[0] ] }
-                        .set { sage_features_input }
-
-                    channel.value("comet").combine(ch_id_comet.combine(ch_mzmls_search, by: 0))
-                        .combine(MSRESCORE_FINE_TUNING.out.model_weight, by:0)
-                        .map { v -> [v[1], v[2], v[3], v[4], v[0] ] }
-                        .set { comet_features_input }
+                    if (params.search_engines.tokenize(",").unique().size() > 1) {
+                        ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage).groupTuple(size: params.search_engines.tokenize(",").unique().size())
+                        .combine(ch_mzmls_search, by: 0)
+                        .combine(MSRESCORE_FINE_TUNING.out.model_weight).set{ ch_id_rescoring }
+                    } else {
+                        ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage).combine(ch_mzmls_search, by: 0)
+                            .combine(MSRESCORE_FINE_TUNING.out.model_weight).set{ ch_id_rescoring }
+                    }
 
-                    MSRESCORE_FEATURES(msgf_features_input.mix(sage_features_input).mix(comet_features_input))
+                    MSRESCORE_FEATURES(ch_id_rescoring)
                     ch_versions = ch_versions.mix(MSRESCORE_FEATURES.out.versions)
                     ch_id_files_feats = MSRESCORE_FEATURES.out.idparquet
 
-
                 }
             } else{
                 if (params.search_engines.tokenize(",").unique().size() > 1) {
@@ -167,8 +139,8 @@ workflow PEPTIDE_DATABASE_SEARCH {
             }
 
         } else if (params.search_engines.tokenize(",").unique().size() > 1) {
-            EXTRACTPSMFEATURES(ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage).groupTuple(size: params.search_engines.tokenize(",").unique().size()))
-            ch_id_files_out = EXTRACTPSMFEATURES.out.id_files_feat
+            PSM_CLEAN(ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage).groupTuple(size: params.search_engines.tokenize(",").unique().size()).combine(ch_mzmls_search, by: 0))
+            ch_id_files_out = PSM_CLEAN.out.idparquet
         } else {
             ch_id_files_out = ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage)
         }
@@ -176,7 +148,7 @@ workflow PEPTIDE_DATABASE_SEARCH {
     } else if (params.psm_clean == true) {
         ch_id_files = ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage)
         PSM_CLEAN(ch_id_files.combine(ch_mzmls_search, by: 0))
-        ch_id_files_out = PSM_CLEAN.out.idxml
+        ch_id_files_out = PSM_CLEAN.out.idparquet
         ch_versions = ch_versions.mix(PSM_CLEAN.out.versions)
     } else {
         ch_id_files_out = ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage)

From 5d1dc3d28b820bd34fb00b27dae8714d9f34969a Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Tue, 9 Jun 2026 15:20:37 +0800
Subject: [PATCH 12/12] update

---
 modules/local/utils/msrescore_features/main.nf     |  4 ++--
 modules/local/utils/msrescore_fine_tuning/main.nf  |  4 ++--
 modules/local/utils/psm_clean/main.nf              |  4 ++--
 subworkflows/local/peptide_database_search/main.nf | 13 ++++++++++++-
 4 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/modules/local/utils/msrescore_features/main.nf b/modules/local/utils/msrescore_features/main.nf
index 2e96d952..449f2fd6 100644
--- a/modules/local/utils/msrescore_features/main.nf
+++ b/modules/local/utils/msrescore_features/main.nf
@@ -3,8 +3,8 @@ process MSRESCORE_FEATURES {
     label 'process_medium'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.17' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.18' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.18' }"
 
     input:
     tuple val(meta), path(id_files), path(mzml), path(model_weight)
diff --git a/modules/local/utils/msrescore_fine_tuning/main.nf b/modules/local/utils/msrescore_fine_tuning/main.nf
index 75a5b5a3..23636619 100644
--- a/modules/local/utils/msrescore_fine_tuning/main.nf
+++ b/modules/local/utils/msrescore_fine_tuning/main.nf
@@ -3,8 +3,8 @@ process MSRESCORE_FINE_TUNING {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.17' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.18' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.18' }"
 
     input:
     tuple val(meta), path(idparquet), path(mzml), path(ms2_model_dir)
diff --git a/modules/local/utils/psm_clean/main.nf b/modules/local/utils/psm_clean/main.nf
index a132e146..650ffc90 100644
--- a/modules/local/utils/psm_clean/main.nf
+++ b/modules/local/utils/psm_clean/main.nf
@@ -3,8 +3,8 @@ process PSM_CLEAN {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.17' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.18' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.18' }"
 
     input:
     tuple val(meta), path(idparquet), path(mzml)
diff --git a/subworkflows/local/peptide_database_search/main.nf b/subworkflows/local/peptide_database_search/main.nf
index fd94db2d..96c8aec3 100644
--- a/subworkflows/local/peptide_database_search/main.nf
+++ b/subworkflows/local/peptide_database_search/main.nf
@@ -91,7 +91,18 @@ workflow PEPTIDE_DATABASE_SEARCH {
                 } else {
 
                     // Preparing train datasets and fine tuning MS2 model
-                    train_datasets = ch_id_sage.mix(ch_id_msgf).mix(ch_id_comet)
+                    // Randomly select one search engine for fine-tuning sampling
+                    engine_opts = []
+                    if (params.search_engines.contains("sage"))  engine_opts.add("sage")
+                    if (params.search_engines.contains("msgf"))  engine_opts.add("msgf")
+                    if (params.search_engines.contains("comet")) engine_opts.add("comet")
+                    selected_engine = engine_opts[new Random(2025).nextInt(engine_opts.size())]
+
+                    ch_selected_engine = (selected_engine == "sage") ? ch_id_sage :
+                                        (selected_engine == "msgf") ? ch_id_msgf :
+                                        ch_id_comet
+
+                    train_datasets = ch_selected_engine
                         .combine(ch_mzmls_search, by: 0)
                         .toSortedList()
                         .flatMap()