Release 3.2.0

.github/workflows/awsfulltest.yml

@@ -37,7 +37,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

.github/workflows/awstest.yml

@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

.github/workflows/download_pipeline.yml

@@ -127,7 +127,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*

.github/workflows/fix_linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

.github/workflows/linting.yml

@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

.github/workflows/nf-test.yml

@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -86,7 +86,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 

.github/workflows/template-version-comment.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 

.gitignore

@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+CLAUDE.md
+.claude/

.nf-core.yml

@@ -2,7 +2,7 @@ lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
     - .vscode/settings.json
-nf_core_version: 3.4.1
+nf_core_version: 3.5.1
 repository_type: pipeline
 template:
   author: Jonas Scheid, Steffen Lemke, Leon Bichmann, Marissa Dubbelaar
@@ -12,7 +12,7 @@ template:
   name: mhcquant
   org: nf-core
   outdir: .
-  version: 3.1.0
   skip_features:
     - fastqc
     - igenomes
+  version: 3.2.0dev

.prettierignore

@@ -12,4 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
-.nf-test/
+modules/nf-core/
+subworkflows/nf-core/

CHANGELOG.md

@@ -3,6 +3,33 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 3.2.0dev - [release name] - [date]
+
+### `Added`
+
+- Added support for single run quantification [#438](https://github.com/nf-core/mhcquant/pull/438)
+- Added per-sample search parameter support via samplesheet with SearchPreset column and individual parameter overrides [#439](https://github.com/nf-core/mhcquant/pull/439)
+- Added ion mobility export and MultiQC distribution plot for timsTOF data [#441](https://github.com/nf-core/mhcquant/pull/441)
+
+### `Fixed`
+
+- Fixed `EPICORE` running only once instead of per sample when `--fasta` is used, by broadcasting `ch_fasta` to `EPICORE` via `.first()` [#446](https://github.com/nf-core/mhcquant/pull/446)
+- Fixed `SUMMARIZE_RESULTS` crash with `--quantify` caused by OpenMS 3.5.0 TextExporter phantom column bug ([OpenMS/OpenMS#9120](https://github.com/OpenMS/OpenMS/issues/9120)) [#444](https://github.com/nf-core/mhcquant/pull/444)
+- Fixed an issue where stripping the sequence in `SUMMARIZE_RESULTS` did not work for complex modifications [#436](https://github.com/nf-core/mhcquant/pull/436)
+
+### `Changed`
+
+- Migrate to topic channels [#431](https://github.com/nf-core/mhcquant/pull/431)
+
+### `Dependencies`
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `easypqp`  | 0.1.53      | 0.1.57      |
+| `MultiQC`  | 1.31.0      | 1.33.0      |
+| `Nf-core`  | 3.4.1       | 3.5.1       |
+| `openms`   | 3.4.1       | 3.5.0       |
+
 ## 3.1.0 - BlüBa - 07/01/26
 
 ### `Added`

README.md

@@ -5,13 +5,13 @@
   </picture>
 </h1>
 
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/mhcquant)
+[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/mhcquant)
 [![GitHub Actions CI Status](https://github.com/nf-core/mhcquant/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/mhcquant/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/mhcquant/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mhcquant/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mhcquant/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.8427707-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.8427707)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

assets/multiqc_config.yml

@@ -3,9 +3,7 @@ custom_logo_url: https://github.com/nf-core/mhcquant
 custom_logo_title: "nf-core/mhcquant"
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/releases/tag/3.1.0" target="_blank">nf-core/mhcquant</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mhcquant/3.1.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/tree/dev" target="_blank">nf-core/mhcquant</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/mhcquant/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mhcquant-methods-description":
     order: -1000
@@ -104,6 +102,19 @@ custom_data:
       xlab: "Retention time"
       ylab: "Frequency"
 
+  im_plot:
+    plot_type: "linegraph"
+    file_format: "csv"
+    section_name: "Ion Mobility"
+    description: |
+      This plot shows the distribution of ion mobility (1/K0) values for identified peptides.
+      Ion mobility data is available when using instruments with ion mobility separation (e.g., timsTOF).
+    pconfig:
+      id: "histogram_im"
+      title: "Ion Mobility Distribution"
+      xlab: "Ion Mobility (1/K0) [V·s/cm²]"
+      ylab: "Frequency"
+
   qvalue_plot:
     plot_type: "linegraph"
     file_format: "csv"
@@ -166,6 +177,8 @@ sp:
     fn: "*_histogram_mz.csv"
   rt_plot:
     fn: "*_histogram_rt.csv"
+  im_plot:
+    fn: "*_histogram_im.csv"
   qvalue_plot:
     fn: "*_histogram_scores.csv"
   scores_plot_xcorr:

assets/schema_input.json

@@ -13,14 +13,14 @@
                 "meta": ["id"]
             },
             "Sample": {
-                "type": "string",
-                "pattern": "^\\S+$",
+                "type": ["string", "integer"],
+                "anyOf": [{ "type": "string", "pattern": "^\\S+$" }, { "type": "integer" }],
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["sample"]
             },
             "Condition": {
-                "type": "string",
-                "pattern": "^\\S+-?",
+                "type": ["string", "integer"],
+                "anyOf": [{ "type": "string", "pattern": "^\\S+-?" }, { "type": "integer" }],
                 "errorMessage": "Sample condition must be provided and cannot contain spaces",
                 "meta": ["condition"]
             },
@@ -37,6 +37,12 @@
                 "exists": true,
                 "pattern": "^\\S+\\.(fasta|fa|fas|fna|faa|ffn)$",
                 "errorMessage": "FASTA file cannot contain spaces and must have one of the extensions: fasta | fa | fas | fna | faa | ffn"
+            },
+            "SearchPreset": {
+                "type": "string",
+                "pattern": "^[a-zA-Z0-9_]+$",
+                "errorMessage": "SearchPreset must contain only alphanumeric characters and underscores",
+                "meta": ["search_preset"]
             }
         },
         "required": ["ID", "Sample", "Condition", "ReplicateFileName"]

assets/schema_search_presets.json

@@ -0,0 +1,125 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/mhcquant/master/assets/schema_search_presets.json",
+    "title": "nf-core/mhcquant pipeline - params.search_presets schema",
+    "description": "Schema for the search parameter presets file provided with params.search_presets",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "PresetName": {
+                "type": "string",
+                "pattern": "^[a-zA-Z0-9_]+$",
+                "errorMessage": "PresetName must contain only alphanumeric characters and underscores",
+                "meta": ["preset_name"]
+            },
+            "PeptideMinLength": {
+                "type": "integer",
+                "minimum": 1,
+                "errorMessage": "PeptideMinLength must be a positive integer",
+                "meta": ["peptide_min_length"]
+            },
+            "PeptideMaxLength": {
+                "type": "integer",
+                "minimum": 1,
+                "errorMessage": "PeptideMaxLength must be a positive integer",
+                "meta": ["peptide_max_length"]
+            },
+            "PrecursorMassRange": {
+                "type": "string",
+                "pattern": "^\\d+:\\d+$",
+                "errorMessage": "PrecursorMassRange must be in format 'min:max' (e.g., '800:2500')",
+                "meta": ["digest_mass_range"]
+            },
+            "PrecursorCharge": {
+                "type": "string",
+                "pattern": "^\\d+:\\d+$",
+                "errorMessage": "PrecursorCharge must be in format 'min:max' (e.g., '2:3')",
+                "meta": ["prec_charge"]
+            },
+            "PrecursorMassTolerance": {
+                "type": "number",
+                "minimum": 0,
+                "errorMessage": "PrecursorMassTolerance must be a non-negative number",
+                "meta": ["precursor_mass_tolerance"]
+            },
+            "PrecursorErrorUnit": {
+                "type": "string",
+                "enum": ["ppm", "Da"],
+                "errorMessage": "PrecursorErrorUnit must be either 'ppm' or 'Da'",
+                "meta": ["precursor_error_units"]
+            },
+            "FragmentMassTolerance": {
+                "type": "number",
+                "minimum": 0,
+                "errorMessage": "FragmentMassTolerance must be a non-negative number",
+                "meta": ["fragment_mass_tolerance"]
+            },
+            "FragmentBinOffset": {
+                "type": "number",
+                "minimum": 0,
+                "errorMessage": "FragmentBinOffset must be a non-negative number",
+                "meta": ["fragment_bin_offset"]
+            },
+            "MS2PIPModel": {
+                "type": "string",
+                "enum": [
+                    "Immuno-HCD",
+                    "timsTOF",
+                    "CIDch2",
+                    "HCD",
+                    "CID",
+                    "ITMS",
+                    "iTRAQ",
+                    "iTRAQphospho",
+                    "TMT",
+                    "HCDch2"
+                ],
+                "errorMessage": "MS2PIPModel must be a valid MS2PIP model name",
+                "meta": ["ms2pip_model"]
+            },
+            "ActivationMethod": {
+                "type": "string",
+                "enum": ["ALL", "CID", "HCD", "ETD", "ECD", "EThcD", "ETciD"],
+                "errorMessage": "ActivationMethod must be one of: ALL, CID, HCD, ETD, ECD, EThcD, ETciD",
+                "meta": ["activation_method"]
+            },
+            "Instrument": {
+                "type": "string",
+                "enum": ["high_res", "low_res"],
+                "errorMessage": "Instrument must be either 'high_res' or 'low_res'",
+                "meta": ["instrument"]
+            },
+            "NumberMods": {
+                "type": "integer",
+                "minimum": 0,
+                "errorMessage": "NumberMods must be a non-negative integer",
+                "meta": ["number_mods"]
+            },
+            "FixedMods": {
+                "type": "string",
+                "errorMessage": "FixedMods must be a comma-separated list of UNIMOD modification names",
+                "meta": ["fixed_mods"]
+            },
+            "VariableMods": {
+                "type": "string",
+                "errorMessage": "VariableMods must be a comma-separated list of UNIMOD modification names",
+                "meta": ["variable_mods"]
+            }
+        },
+        "required": [
+            "PresetName",
+            "PeptideMinLength",
+            "PeptideMaxLength",
+            "PrecursorMassRange",
+            "PrecursorCharge",
+            "PrecursorMassTolerance",
+            "FragmentMassTolerance",
+            "FragmentBinOffset",
+            "MS2PIPModel",
+            "ActivationMethod",
+            "Instrument",
+            "NumberMods"
+        ]
+    }
+}

assets/search_presets.tsv

@@ -0,0 +1,11 @@
+PresetName	PeptideMinLength	PeptideMaxLength	PrecursorMassRange	PrecursorCharge	PrecursorMassTolerance	PrecursorErrorUnit	FragmentMassTolerance	FragmentBinOffset	MS2PIPModel	ActivationMethod	Instrument	NumberMods	FixedMods	VariableMods
+lumos_class1	8	14	800:2500	2:3	5	ppm	0.01	0.0	Immuno-HCD	HCD	high_res	3	 	Oxidation (M)
+lumos_class2	8	30	800:5000	2:5	5	ppm	0.01	0.0	Immuno-HCD	HCD	high_res	5	 	Oxidation (M)
+qe_class1	8	14	800:2500	2:3	5	ppm	0.01	0.0	Immuno-HCD	HCD	high_res	3	 	Oxidation (M)
+qe_class2	8	30	800:5000	2:5	5	ppm	0.01	0.0	Immuno-HCD	HCD	high_res	5	 	Oxidation (M)
+timstof_class1	8	14	800:2500	1:4	20	ppm	0.01	0.0	timsTOF	CID	high_res	3	 	Oxidation (M)
+timstof_class2	8	30	800:5000	1:5	20	ppm	0.01	0.0	timsTOF	CID	high_res	5	 	Oxidation (M)
+astral_class1	8	14	800:2500	2:3	5	ppm	0.01	0.0	Immuno-HCD	HCD	high_res	3	 	Oxidation (M)
+astral_class2	8	30	800:5000	2:5	5	ppm	0.01	0.0	Immuno-HCD	HCD	high_res	5	 	Oxidation (M)
+xl_class1	8	14	800:2500	2:3	5	ppm	0.50025	0.4	CIDch2	CID	low_res	3	 	Oxidation (M)
+xl_class2	8	30	800:5000	2:5	5	ppm	0.50025	0.4	CIDch2	CID	low_res	5	 	Oxidation (M)