From 2de69b350c10821c5bd00400b03d6ff863334a20 Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Mon, 30 Mar 2026 13:47:58 +0000
Subject: [PATCH 1/7] adding Percolator module

---
 modules/nf-core/percolator/environment.yml    |   7 ++
 modules/nf-core/percolator/main.nf            |  46 +++++++
 modules/nf-core/percolator/meta.yml           |  80 ++++++++++++
 modules/nf-core/percolator/tests/main.nf.test |  54 ++++++++
 .../percolator/tests/main.nf.test.snap        | 116 ++++++++++++++++++
 5 files changed, 303 insertions(+)
 create mode 100644 modules/nf-core/percolator/environment.yml
 create mode 100644 modules/nf-core/percolator/main.nf
 create mode 100644 modules/nf-core/percolator/meta.yml
 create mode 100644 modules/nf-core/percolator/tests/main.nf.test
 create mode 100644 modules/nf-core/percolator/tests/main.nf.test.snap

diff --git a/modules/nf-core/percolator/environment.yml b/modules/nf-core/percolator/environment.yml
new file mode 100644
index 000000000000..966fe62ad107
--- /dev/null
+++ b/modules/nf-core/percolator/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::percolator=3.7.1"
diff --git a/modules/nf-core/percolator/main.nf b/modules/nf-core/percolator/main.nf
new file mode 100644
index 000000000000..2fce6be4c8a9
--- /dev/null
+++ b/modules/nf-core/percolator/main.nf
@@ -0,0 +1,46 @@
+process PERCOLATOR {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/percolator:3.7.1--h6351f2a_0'
+        : 'biocontainers/percolator:3.7.1--h6351f2a_0'}"
+
+    input:
+    tuple val(meta), path(peptide_identification)
+
+    output:
+    tuple val(meta), path("*.target.pout"), emit: target_pout
+    tuple val(meta), path("*.decoy.pout"), emit: decoy_pout
+
+    tuple val("${task.process}"), val('percolator'), eval('percolator --help 2>&1 | head -1 | sed "s;Percolator version \\([^,]*\\),.*;\\1;"'), topic: versions, emit: versions_percolator
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    percolator \\
+        ${args} \\
+        --num-threads ${task.cpus} \\
+        --only-psms \\
+        --post-processing-tdc \\
+        --search-input concatenated \\
+        --results-psms ${prefix}.psm.target.pout \\
+        --decoy-results-psms ${prefix}.psm.decoy.pout \\
+        ${peptide_identification}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+
+    touch ${prefix}.psm.target.pout
+    touch ${prefix}.psm.decoy.pout
+    """
+}
diff --git a/modules/nf-core/percolator/meta.yml b/modules/nf-core/percolator/meta.yml
new file mode 100644
index 000000000000..93354d491ac8
--- /dev/null
+++ b/modules/nf-core/percolator/meta.yml
@@ -0,0 +1,80 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "percolator"
+description: Rescore peptide-spectrum matches and estimate false discovery rates using the Percolator semi-supervised learning algorithm.
+keywords:
+  - proteomics
+  - spectrum identification
+  - psm
+  - rescoring
+  - false discovery rate
+  - features
+tools:
+  - "percolator":
+      description: "Semi-supervised learning for peptide identification from shotgun
+        proteomics datasets."
+      homepage: "http://percolator.ms"
+      documentation: "http://percolator.ms"
+      tool_dev_url: "https://github.com/percolator/percolator"
+      doi: "10.1038/nmeth1113"
+      licence: ["Apache-2.0"]
+      identifier: biotools:percolator
+
+input:
+  - - meta:
+        type: map
+        description: Groovy Map containing sample information. e.g. `[
+          id:'sample1' ]`
+    - peptide_identification:
+        type: file
+        description: peptide identifications as PIN file
+        pattern: "*.{pin}"
+        ontologies: []
+
+output:
+  target_pout:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[
+            id:'sample1' ]`
+      - "*.target.pout":
+          type: file
+          description: percolator output file containing the target PSMs
+          pattern: "*.{target.pout}"
+          ontologies: []
+
+  decoy_pout:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[
+            id:'sample1' ]`
+      - "*.decoy.pout":
+          type: file
+          description: percolator output file containing the decoys PSMs
+          pattern: "*.{decoy.pout}"
+          ontologies: []
+
+  versions_percolator:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - percolator:
+          type: string
+          description: The name of the tool
+      - percolator --help 2>&1 | head -1 | sed "s;Percolator version \([^,]*\),.*;\1;":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - percolator:
+          type: string
+          description: The name of the tool
+      - percolator --help 2>&1 | head -1 | sed "s;Percolator version \([^,]*\),.*;\1;":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@julianu"
+maintainers:
+  - "@julianu"
diff --git a/modules/nf-core/percolator/tests/main.nf.test b/modules/nf-core/percolator/tests/main.nf.test
new file mode 100644
index 000000000000..f7348d377245
--- /dev/null
+++ b/modules/nf-core/percolator/tests/main.nf.test
@@ -0,0 +1,54 @@
+nextflow_process {
+
+    name "Test Process PERCOLATOR"
+    script "../main.nf"
+    process "PERCOLATOR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "percolator"
+
+    test("percolator - OVEMB150205_12.pin") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file('https://raw.githubusercontent.com/medbioinf/test-datasets/refs/heads/percolator_tests/data/proteomics/percolator/OVEMB150205_12.pin', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    
+    test("percolator - OVEMB150205_12.pin - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file('https://raw.githubusercontent.com/medbioinf/test-datasets/refs/heads/percolator_tests/data/proteomics/percolator/OVEMB150205_12.pin', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/percolator/tests/main.nf.test.snap b/modules/nf-core/percolator/tests/main.nf.test.snap
new file mode 100644
index 000000000000..bd4e38638869
--- /dev/null
+++ b/modules/nf-core/percolator/tests/main.nf.test.snap
@@ -0,0 +1,116 @@
+{
+    "percolator - OVEMB150205_12.pin - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.target.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.decoy.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        "PERCOLATOR",
+                        "percolator",
+                        "3.07.1"
+                    ]
+                ],
+                "decoy_pout": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.decoy.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "target_pout": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.target.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_percolator": [
+                    [
+                        "PERCOLATOR",
+                        "percolator",
+                        "3.07.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-30T13:40:12.100601718",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "percolator - OVEMB150205_12.pin": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.target.pout:md5,7e8293ede65b0ffbff1e8fcd49cf7109"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.decoy.pout:md5,d5a63245b8efac18577df7b8fea58c91"
+                    ]
+                ],
+                "2": [
+                    [
+                        "PERCOLATOR",
+                        "percolator",
+                        "3.07.1"
+                    ]
+                ],
+                "decoy_pout": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.decoy.pout:md5,d5a63245b8efac18577df7b8fea58c91"
+                    ]
+                ],
+                "target_pout": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.target.pout:md5,7e8293ede65b0ffbff1e8fcd49cf7109"
+                    ]
+                ],
+                "versions_percolator": [
+                    [
+                        "PERCOLATOR",
+                        "percolator",
+                        "3.07.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-30T13:40:07.137394818",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file

From d91864bf7e4abdfcd01294267dd84304cddc9112 Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Thu, 23 Apr 2026 10:47:06 +0000
Subject: [PATCH 2/7] setup required tests

---
 modules/nf-core/percolator/main.nf            | 14 ++---
 modules/nf-core/percolator/meta.yml           | 15 +++---
 modules/nf-core/percolator/tests/main.nf.test | 51 +++++++++++++++----
 .../percolator/tests/main.nf.test.snap        | 12 ++---
 4 files changed, 61 insertions(+), 31 deletions(-)

diff --git a/modules/nf-core/percolator/main.nf b/modules/nf-core/percolator/main.nf
index 2fce6be4c8a9..bbdd83106c9c 100644
--- a/modules/nf-core/percolator/main.nf
+++ b/modules/nf-core/percolator/main.nf
@@ -1,5 +1,5 @@
 process PERCOLATOR {
-    tag "${meta.id}"
+    tag "$meta.id"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -11,9 +11,8 @@ process PERCOLATOR {
     tuple val(meta), path(peptide_identification)
 
     output:
-    tuple val(meta), path("*.target.pout"), emit: target_pout
-    tuple val(meta), path("*.decoy.pout"), emit: decoy_pout
-
+    tuple val(meta), path("${prefix}.psm.target.pout"), emit: target_pout
+    tuple val(meta), path("${prefix}.psm.decoy.pout"), emit: decoy_pout
     tuple val("${task.process}"), val('percolator'), eval('percolator --help 2>&1 | head -1 | sed "s;Percolator version \\([^,]*\\),.*;\\1;"'), topic: versions, emit: versions_percolator
 
     when:
@@ -21,7 +20,7 @@ process PERCOLATOR {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     percolator \\
         ${args} \\
@@ -35,11 +34,8 @@ process PERCOLATOR {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
-    echo ${args}
-
     touch ${prefix}.psm.target.pout
     touch ${prefix}.psm.decoy.pout
     """
diff --git a/modules/nf-core/percolator/meta.yml b/modules/nf-core/percolator/meta.yml
index 93354d491ac8..675a62571dc0 100644
--- a/modules/nf-core/percolator/meta.yml
+++ b/modules/nf-core/percolator/meta.yml
@@ -26,8 +26,8 @@ input:
           id:'sample1' ]`
     - peptide_identification:
         type: file
-        description: peptide identifications as PIN file
-        pattern: "*.{pin}"
+        description: peptide identifications as PIN (Percolator input) file
+        pattern: "*.pin"
         ontologies: []
 
 output:
@@ -36,10 +36,10 @@ output:
           type: map
           description: Groovy Map containing sample information. e.g. `[
             id:'sample1' ]`
-      - "*.target.pout":
+      - "${prefix}.psm.target.pout":
           type: file
           description: percolator output file containing the target PSMs
-          pattern: "*.{target.pout}"
+          pattern: "*.pout"
           ontologies: []
 
   decoy_pout:
@@ -47,10 +47,10 @@ output:
           type: map
           description: Groovy Map containing sample information. e.g. `[
             id:'sample1' ]`
-      - "*.decoy.pout":
+      - "${prefix}.psm.decoy.pout":
           type: file
           description: percolator output file containing the decoys PSMs
-          pattern: "*.{decoy.pout}"
+          pattern: "*.pout"
           ontologies: []
 
   versions_percolator:
@@ -60,9 +60,10 @@ output:
       - percolator:
           type: string
           description: The name of the tool
-      - percolator --help 2>&1 | head -1 | sed "s;Percolator version \([^,]*\),.*;\1;":
+      - "percolator --help 2>&1 | head -1 | sed 's;Percolator version \\([^,]*\\),.*;\\1;'":
           type: eval
           description: The expression to obtain the version of the tool
+
 topics:
   versions:
     - - ${task.process}:
diff --git a/modules/nf-core/percolator/tests/main.nf.test b/modules/nf-core/percolator/tests/main.nf.test
index f7348d377245..a58057eb3185 100644
--- a/modules/nf-core/percolator/tests/main.nf.test
+++ b/modules/nf-core/percolator/tests/main.nf.test
@@ -7,15 +7,52 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "percolator"
+    tag "comet"
+    tag "openms/decoydatabase"
+
+    setup {
+        run("OPENMS_DECOYDATABASE") {
+            script "../../openms/decoydatabase/main.nf"
+            process {
+                """
+                input[0] = channel.of([
+                    [ id:'test_db' ],
+                    file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists: true),
+                ])
+                """
+            }
+        }
+
+        run("COMET") {
+            script "../../comet/main.nf"
+
+            process {
+                """
+                def originalParams = file(params.modules_testdata_base_path + 'proteomics/parameter/OVEMB150205.comet.params', checkIfExists: true)
+                def modifiedParams = new File('./modified.comet.params')
+                modifiedParams.text = originalParams.text
+                    .replaceAll('(?m)^output_percolatorfile =.*', 'output_percolatorfile = 1')
+                    .replaceAll('(?m)^output_txtfile =.*', 'output_txtfile = 0')
+                    .replaceAll('(?m)^output_mzidentmlfile =.*', 'output_mzidentmlfile = 0')
+
+                input[0] = OPENMS_DECOYDATABASE.out.decoy_fasta.map { meta, fasta ->
+                    [
+                        [ id:'test'],
+                        file(params.modules_testdata_base_path + 'proteomics/msspectra/OVEMB150205_12.mzML', checkIfExists: true),
+                        fasta,
+                        file(modifiedParams),
+                    ]
+                }
+                """
+            }
+        }
+    }
 
     test("percolator - OVEMB150205_12.pin") {
         when {
             process {
                 """
-                input[0] = [
-                    [ id:'test' ],
-                    file('https://raw.githubusercontent.com/medbioinf/test-datasets/refs/heads/percolator_tests/data/proteomics/percolator/OVEMB150205_12.pin', checkIfExists: true),
-                ]
+                input[0] = COMET.out.pin
                 """
             }
         }
@@ -27,7 +64,6 @@ nextflow_process {
             )
         }
     }
-
     
     test("percolator - OVEMB150205_12.pin - stub") {
 
@@ -36,10 +72,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [
-                    [ id:'test' ],
-                    file('https://raw.githubusercontent.com/medbioinf/test-datasets/refs/heads/percolator_tests/data/proteomics/percolator/OVEMB150205_12.pin', checkIfExists: true),
-                ]
+                input[0] = COMET.out.pin
                 """
             }
         }
diff --git a/modules/nf-core/percolator/tests/main.nf.test.snap b/modules/nf-core/percolator/tests/main.nf.test.snap
index bd4e38638869..3dd89ec49c32 100644
--- a/modules/nf-core/percolator/tests/main.nf.test.snap
+++ b/modules/nf-core/percolator/tests/main.nf.test.snap
@@ -50,7 +50,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-30T13:40:12.100601718",
+        "timestamp": "2026-04-23T10:35:47.104947826",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -64,7 +64,7 @@
                         {
                             "id": "test"
                         },
-                        "test.psm.target.pout:md5,7e8293ede65b0ffbff1e8fcd49cf7109"
+                        "test.psm.target.pout:md5,61d48fdb8597aa5b5dde5c41b0cf1721"
                     ]
                 ],
                 "1": [
@@ -72,7 +72,7 @@
                         {
                             "id": "test"
                         },
-                        "test.psm.decoy.pout:md5,d5a63245b8efac18577df7b8fea58c91"
+                        "test.psm.decoy.pout:md5,7c9909537ccb675680e02504f07f2a74"
                     ]
                 ],
                 "2": [
@@ -87,7 +87,7 @@
                         {
                             "id": "test"
                         },
-                        "test.psm.decoy.pout:md5,d5a63245b8efac18577df7b8fea58c91"
+                        "test.psm.decoy.pout:md5,7c9909537ccb675680e02504f07f2a74"
                     ]
                 ],
                 "target_pout": [
@@ -95,7 +95,7 @@
                         {
                             "id": "test"
                         },
-                        "test.psm.target.pout:md5,7e8293ede65b0ffbff1e8fcd49cf7109"
+                        "test.psm.target.pout:md5,61d48fdb8597aa5b5dde5c41b0cf1721"
                     ]
                 ],
                 "versions_percolator": [
@@ -107,7 +107,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-30T13:40:07.137394818",
+        "timestamp": "2026-04-23T10:35:41.387430243",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From 23074339e8f1fbeb9a1646cee7e0e33e3508c565 Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Thu, 23 Apr 2026 11:02:50 +0000
Subject: [PATCH 3/7] fixing linter issues

---
 modules/nf-core/percolator/meta.yml           | 20 ++++++++-----------
 modules/nf-core/percolator/tests/main.nf.test |  2 +-
 2 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/percolator/meta.yml b/modules/nf-core/percolator/meta.yml
index 675a62571dc0..57259cd124de 100644
--- a/modules/nf-core/percolator/meta.yml
+++ b/modules/nf-core/percolator/meta.yml
@@ -1,6 +1,6 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "percolator"
-description: Rescore peptide-spectrum matches and estimate false discovery rates using the Percolator semi-supervised learning algorithm.
+description: Rescore peptide-spectrum matches and estimate false discovery rates
+  using the Percolator semi-supervised learning algorithm.
 keywords:
   - proteomics
   - spectrum identification
@@ -22,37 +22,34 @@ tools:
 input:
   - - meta:
         type: map
-        description: Groovy Map containing sample information. e.g. `[
+        description: Groovy Map containing sample information. e.g. `[ 
           id:'sample1' ]`
     - peptide_identification:
         type: file
         description: peptide identifications as PIN (Percolator input) file
         pattern: "*.pin"
         ontologies: []
-
 output:
   target_pout:
     - - meta:
           type: map
-          description: Groovy Map containing sample information. e.g. `[
+          description: Groovy Map containing sample information. e.g. `[ 
             id:'sample1' ]`
-      - "${prefix}.psm.target.pout":
+      - ${prefix}.psm.target.pout:
           type: file
           description: percolator output file containing the target PSMs
           pattern: "*.pout"
           ontologies: []
-
   decoy_pout:
     - - meta:
           type: map
-          description: Groovy Map containing sample information. e.g. `[
+          description: Groovy Map containing sample information. e.g. `[ 
             id:'sample1' ]`
-      - "${prefix}.psm.decoy.pout":
+      - ${prefix}.psm.decoy.pout:
           type: file
           description: percolator output file containing the decoys PSMs
           pattern: "*.pout"
           ontologies: []
-
   versions_percolator:
     - - ${task.process}:
           type: string
@@ -60,10 +57,9 @@ output:
       - percolator:
           type: string
           description: The name of the tool
-      - "percolator --help 2>&1 | head -1 | sed 's;Percolator version \\([^,]*\\),.*;\\1;'":
+      - percolator --help 2>&1 | head -1 | sed "s;Percolator version \([^,]*\),.*;\1;":
           type: eval
           description: The expression to obtain the version of the tool
-
 topics:
   versions:
     - - ${task.process}:
diff --git a/modules/nf-core/percolator/tests/main.nf.test b/modules/nf-core/percolator/tests/main.nf.test
index a58057eb3185..5713149d08a8 100644
--- a/modules/nf-core/percolator/tests/main.nf.test
+++ b/modules/nf-core/percolator/tests/main.nf.test
@@ -64,7 +64,7 @@ nextflow_process {
             )
         }
     }
-    
+
     test("percolator - OVEMB150205_12.pin - stub") {
 
         options "-stub"

From b4a5093274adf31e7d72e72b91b64471afcdb27e Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Thu, 23 Apr 2026 12:03:53 +0000
Subject: [PATCH 4/7] fix linter issue

---
 modules/nf-core/percolator/meta.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/percolator/meta.yml b/modules/nf-core/percolator/meta.yml
index 57259cd124de..ec577c67e586 100644
--- a/modules/nf-core/percolator/meta.yml
+++ b/modules/nf-core/percolator/meta.yml
@@ -22,7 +22,7 @@ tools:
 input:
   - - meta:
         type: map
-        description: Groovy Map containing sample information. e.g. `[ 
+        description: Groovy Map containing sample information. e.g. `[
           id:'sample1' ]`
     - peptide_identification:
         type: file
@@ -33,7 +33,7 @@ output:
   target_pout:
     - - meta:
           type: map
-          description: Groovy Map containing sample information. e.g. `[ 
+          description: Groovy Map containing sample information. e.g. `[
             id:'sample1' ]`
       - ${prefix}.psm.target.pout:
           type: file
@@ -43,7 +43,7 @@ output:
   decoy_pout:
     - - meta:
           type: map
-          description: Groovy Map containing sample information. e.g. `[ 
+          description: Groovy Map containing sample information. e.g. `[
             id:'sample1' ]`
       - ${prefix}.psm.decoy.pout:
           type: file

From 274ccae4a61a5b17f2f818e2cc5bcacf9ca8e0bd Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Thu, 23 Apr 2026 12:10:08 +0000
Subject: [PATCH 5/7] adding container prefix

---
 modules/nf-core/percolator/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/percolator/main.nf b/modules/nf-core/percolator/main.nf
index bbdd83106c9c..768c4c45c8fa 100644
--- a/modules/nf-core/percolator/main.nf
+++ b/modules/nf-core/percolator/main.nf
@@ -5,7 +5,7 @@ process PERCOLATOR {
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'https://depot.galaxyproject.org/singularity/percolator:3.7.1--h6351f2a_0'
-        : 'biocontainers/percolator:3.7.1--h6351f2a_0'}"
+        : 'quay.io/biocontainers/percolator:3.7.1--h6351f2a_0'}"
 
     input:
     tuple val(meta), path(peptide_identification)

From fd9525c81e5259b71f672644d004256a4c04aeab Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Thu, 23 Apr 2026 16:00:47 +0000
Subject: [PATCH 6/7] sanitizing output

---
 modules/nf-core/percolator/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/percolator/tests/main.nf.test b/modules/nf-core/percolator/tests/main.nf.test
index 5713149d08a8..143ef83eeb4a 100644
--- a/modules/nf-core/percolator/tests/main.nf.test
+++ b/modules/nf-core/percolator/tests/main.nf.test
@@ -60,7 +60,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -80,7 +80,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

From b2de6952ae334a6ce3fc6b5db7dd65feb230ef3f Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Thu, 23 Apr 2026 18:39:07 +0000
Subject: [PATCH 7/7] fetching all of percolators outputs and adapting tests
 accordingly

---
 modules/nf-core/percolator/main.nf            |  31 +++++-
 modules/nf-core/percolator/meta.yml           |  94 ++++++++++++++--
 modules/nf-core/percolator/tests/main.nf.test |  16 ++-
 .../percolator/tests/main.nf.test.snap        | 105 ++++++++++++------
 4 files changed, 193 insertions(+), 53 deletions(-)

diff --git a/modules/nf-core/percolator/main.nf b/modules/nf-core/percolator/main.nf
index 768c4c45c8fa..cfcc0783f9ef 100644
--- a/modules/nf-core/percolator/main.nf
+++ b/modules/nf-core/percolator/main.nf
@@ -11,8 +11,16 @@ process PERCOLATOR {
     tuple val(meta), path(peptide_identification)
 
     output:
-    tuple val(meta), path("${prefix}.psm.target.pout"), emit: target_pout
-    tuple val(meta), path("${prefix}.psm.decoy.pout"), emit: decoy_pout
+    tuple val(meta), path("${prefix}.pout.xml"), emit: pout_xml
+    tuple val(meta), path("${prefix}.pep.xml"), emit: pout_pepxml
+    tuple val(meta), path("${prefix}.features.pin"), emit: features_pin
+    tuple val(meta), path("${prefix}.weights.tsv"), emit: weights
+    tuple val(meta), path("${prefix}.pep.target.pout"), emit: target_peptides, optional: true
+    tuple val(meta), path("${prefix}.pep.decoy.pout"), emit: decoy_peptides, optional: true
+    tuple val(meta), path("${prefix}.psm.target.pout"), emit: target_psms
+    tuple val(meta), path("${prefix}.psm.decoy.pout"), emit: decoy_psms
+    tuple val(meta), path("${prefix}.protein.target.pout"), emit: target_proteins, optional: true
+    tuple val(meta), path("${prefix}.protein.decoy.pout"), emit: decoy_proteins, optional: true
     tuple val("${task.process}"), val('percolator'), eval('percolator --help 2>&1 | head -1 | sed "s;Percolator version \\([^,]*\\),.*;\\1;"'), topic: versions, emit: versions_percolator
 
     when:
@@ -25,18 +33,31 @@ process PERCOLATOR {
     percolator \\
         ${args} \\
         --num-threads ${task.cpus} \\
-        --only-psms \\
-        --post-processing-tdc \\
-        --search-input concatenated \\
+        --xmloutput ${prefix}.pout.xml \\
+        --pepxml-output ${prefix}.pep.xml \\
+        --tab-out ${prefix}.features.pin \\
+        --weights ${prefix}.weights.tsv \\
+        --results-peptides ${prefix}.pep.target.pout \\
+        --decoy-results-peptides ${prefix}.pep.decoy.pout \\
         --results-psms ${prefix}.psm.target.pout \\
         --decoy-results-psms ${prefix}.psm.decoy.pout \\
+        --results-proteins ${prefix}.protein.target.pout \\
+        --decoy-results-proteins ${prefix}.protein.decoy.pout \\
         ${peptide_identification}
     """
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
     """
+    touch ${prefix}.pout.xml
+    touch ${prefix}.pep.xml
+    touch ${prefix}.features.pin
+    touch ${prefix}.weights.tsv
+    touch ${prefix}.pep.target.pout
+    touch ${prefix}.pep.decoy.pout
     touch ${prefix}.psm.target.pout
     touch ${prefix}.psm.decoy.pout
+    touch ${prefix}.protein.target.pout
+    touch ${prefix}.protein.decoy.pout
     """
 }
diff --git a/modules/nf-core/percolator/meta.yml b/modules/nf-core/percolator/meta.yml
index ec577c67e586..b057e827b943 100644
--- a/modules/nf-core/percolator/meta.yml
+++ b/modules/nf-core/percolator/meta.yml
@@ -5,6 +5,8 @@ keywords:
   - proteomics
   - spectrum identification
   - psm
+  - peptide
+  - protein
   - rescoring
   - false discovery rate
   - features
@@ -30,25 +32,97 @@ input:
         pattern: "*.pin"
         ontologies: []
 output:
-  target_pout:
+  pout_xml:
     - - meta:
           type: map
-          description: Groovy Map containing sample information. e.g. `[
-            id:'sample1' ]`
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+      - ${prefix}.pout.xml:
+          type: file
+          description: Percolator output in XML format containing all PSM-level results
+          pattern: "*.pout.xml"
+          ontologies:
+            - edam: "http://edamontology.org/format_2332" # XML
+  pout_pepxml:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+      - ${prefix}.pep.xml:
+          type: file
+          description: Percolator output in pepXML format
+          pattern: "*.pep.xml"
+          ontologies:
+            - edam: "http://edamontology.org/format_3655" # pepXML
+  features_pin:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+      - ${prefix}.features.pin:
+          type: file
+          description: Tab-separated file with rescored features (PIN format)
+          pattern: "*.features.pin"
+          ontologies: []
+  weights:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+      - ${prefix}.weights.tsv:
+          type: file
+          description: TSV file containing the final feature weights
+          pattern: "*.weights.tsv"
+          ontologies: []
+  target_peptides:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+      - ${prefix}.pep.target.pout:
+          type: file
+          description: Target peptide-level results in tab separated format (pout)
+          pattern: "*.pep.target.pout"
+          ontologies: []
+  decoy_peptides:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+      - ${prefix}.pep.decoy.pout:
+          type: file
+          description: Decoy peptide-level results in tab separated format (pout)
+          pattern: "*.pep.decoy.pout"
+          ontologies: []
+  target_psms:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
       - ${prefix}.psm.target.pout:
           type: file
-          description: percolator output file containing the target PSMs
-          pattern: "*.pout"
+          description: Target PSM-level results in tab separated format (pout)
+          pattern: "*.psm.target.pout"
           ontologies: []
-  decoy_pout:
+  decoy_psms:
     - - meta:
           type: map
-          description: Groovy Map containing sample information. e.g. `[
-            id:'sample1' ]`
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
       - ${prefix}.psm.decoy.pout:
           type: file
-          description: percolator output file containing the decoys PSMs
-          pattern: "*.pout"
+          description: Decoy PSM-level results in tab separated format (pout)
+          pattern: "*.psm.decoy.pout"
+          ontologies: []
+  target_proteins:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+      - ${prefix}.protein.target.pout:
+          type: file
+          description: Target protein-level results in tab separated format (pout)
+          pattern: "*.protein.target.pout"
+          ontologies: []
+  decoy_proteins:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
+      - ${prefix}.protein.decoy.pout:
+          type: file
+          description: Decoy protein-level results in tab separated format (pout)
+          pattern: "*.protein.decoy.pout"
           ontologies: []
   versions_percolator:
     - - ${task.process}:
diff --git a/modules/nf-core/percolator/tests/main.nf.test b/modules/nf-core/percolator/tests/main.nf.test
index 143ef83eeb4a..f32c0193bd57 100644
--- a/modules/nf-core/percolator/tests/main.nf.test
+++ b/modules/nf-core/percolator/tests/main.nf.test
@@ -48,7 +48,7 @@ nextflow_process {
         }
     }
 
-    test("percolator - OVEMB150205_12.pin") {
+    test("percolator - OVEMB150205_12") {
         when {
             process {
                 """
@@ -58,14 +58,24 @@ nextflow_process {
         }
 
         then {
+            def outputs = sanitizeOutput(process.out).findAll { key, val ->
+                ['pout_xml', 'features_pin', 'weights', 'target_psms', 'decoy_psms'].contains(key)
+            }
+
             assertAll(
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match() }
+                // all but pepXML can be matched as whole, pepXML has a timestamp and must be treated separately
+                { assert snapshot(outputs).match() },
+                // in pepXML: check some lines for existence
+                { assert path(process.out.pout_pepxml.get(0).get(1)).readLines().any { it.contains('<spectrum_query spectrum="test_98_3_1"') }},
+                { assert path(process.out.pout_pepxml.get(0).get(1)).readLines().any { it.contains('</msms_pipeline_analysis>') }}
+
             )
+
         }
     }
 
-    test("percolator - OVEMB150205_12.pin - stub") {
+    test("percolator - OVEMB150205_12 - stub") {
 
         options "-stub"
 
diff --git a/modules/nf-core/percolator/tests/main.nf.test.snap b/modules/nf-core/percolator/tests/main.nf.test.snap
index 3dd89ec49c32..ff41981f14af 100644
--- a/modules/nf-core/percolator/tests/main.nf.test.snap
+++ b/modules/nf-core/percolator/tests/main.nf.test.snap
@@ -1,101 +1,128 @@
 {
-    "percolator - OVEMB150205_12.pin - stub": {
+    "percolator - OVEMB150205_12": {
         "content": [
             {
-                "0": [
+                "decoy_psms": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.psm.target.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.psm.decoy.pout:md5,7c9909537ccb675680e02504f07f2a74"
                     ]
                 ],
-                "1": [
+                "features_pin": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.psm.decoy.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        "PERCOLATOR",
-                        "percolator",
-                        "3.07.1"
+                        "test.features.pin:md5,4f49bdcb40d891c8bfb61f794465d1be"
                     ]
                 ],
-                "decoy_pout": [
+                "pout_xml": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.psm.decoy.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.pout.xml:md5,6a6be470f5961d54f2ee6c9c8596a476"
                     ]
                 ],
-                "target_pout": [
+                "target_psms": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.psm.target.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.psm.target.pout:md5,61d48fdb8597aa5b5dde5c41b0cf1721"
                     ]
                 ],
-                "versions_percolator": [
+                "weights": [
                     [
-                        "PERCOLATOR",
-                        "percolator",
-                        "3.07.1"
+                        {
+                            "id": "test"
+                        },
+                        "test.weights.tsv:md5,359b4a49c53892bef1738ae693520f69"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-04-23T10:35:47.104947826",
+        "timestamp": "2026-04-23T18:13:39.425266156",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
         }
     },
-    "percolator - OVEMB150205_12.pin": {
+    "percolator - OVEMB150205_12 - stub": {
         "content": [
             {
-                "0": [
+                "decoy_peptides": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.psm.target.pout:md5,61d48fdb8597aa5b5dde5c41b0cf1721"
+                        "test.pep.decoy.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
+                "decoy_proteins": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.psm.decoy.pout:md5,7c9909537ccb675680e02504f07f2a74"
+                        "test.protein.decoy.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "2": [
+                "decoy_psms": [
                     [
-                        "PERCOLATOR",
-                        "percolator",
-                        "3.07.1"
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.decoy.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "decoy_pout": [
+                "features_pin": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.psm.decoy.pout:md5,7c9909537ccb675680e02504f07f2a74"
+                        "test.features.pin:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "target_pout": [
+                "pout_pepxml": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.psm.target.pout:md5,61d48fdb8597aa5b5dde5c41b0cf1721"
+                        "test.pep.xml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pout_xml": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pout.xml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "target_peptides": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pep.target.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "target_proteins": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.protein.target.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "target_psms": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.psm.target.pout:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions_percolator": [
@@ -104,10 +131,18 @@
                         "percolator",
                         "3.07.1"
                     ]
+                ],
+                "weights": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.weights.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ]
             }
         ],
-        "timestamp": "2026-04-23T10:35:41.387430243",
+        "timestamp": "2026-04-23T18:13:45.966539564",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"