Release 3.2.0 prep: PR #447 review fixes + textexporter migration

.nf-core.yml

@@ -15,4 +15,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: 3.2.0dev
+  version: 3.2.0

CHANGELOG.md

@@ -3,23 +3,34 @@
 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]
+## 3.2.0 - Solitude - 23/04/26
 
 ### `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 per-sample search parameter support via samplesheet with SearchPreset column [#439](https://github.com/nf-core/mhcquant/pull/439)
+- Added PRIDE ID and SDRF sheet support [#445](https://github.com/nf-core/mhcquant/pull/445)
 - 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)
+- Fixed `tdf2mzml` container entrypoint issue by pinning to `0.5_noentry` and invoking the CLI explicitly [#447](https://github.com/nf-core/mhcquant/pull/447)
+- Fixed `OPENMS_FILECONVERTER` version extraction emitting a SOH byte due to a single-backslash sed backreference [#447](https://github.com/nf-core/mhcquant/pull/447)
+- Fixed `OPENMS_IDMASSACCURACY` process argument to use `meta.precursor_error_units` so per-sample preset overrides apply [#447](https://github.com/nf-core/mhcquant/pull/447)
 
 ### `Changed`
 
 - Migrate to topic channels [#431](https://github.com/nf-core/mhcquant/pull/431)
+- Bumped `openms/fileconverter`, `openms/featurefinderidentification` and `openms/idconflictresolver` local modules to OpenMS 3.5.0 [#447](https://github.com/nf-core/mhcquant/pull/447)
+- Rewrote `openms/idmassaccuracy` meta.yml to reflect the actual process I/O [#447](https://github.com/nf-core/mhcquant/pull/447)
+- Tightened preset normalization so empty/whitespace `FixedMods` and `VariableMods` cells are treated as empty (preserves the existing `-fixed_modifications` CLI call) [#447](https://github.com/nf-core/mhcquant/pull/447)
+- Migrated `conf/test_single_quant.config` from deprecated `max_cpus`/`max_memory`/`max_time` to `process.resourceLimits` [#447](https://github.com/nf-core/mhcquant/pull/447)
+- Replaced local `openms/textexporter` module with the `nf-core/modules` equivalent; preserved the `_exported` output suffix via `ext.prefix` to keep SUMMARIZE_RESULTS input/output filenames distinct [#447](https://github.com/nf-core/mhcquant/pull/447)
+- Replaced local `openms/fileconverter` module with the `nf-core/modules` equivalent; updated `PROCESS_FEATURE` to consume the renamed `converted` output channel [#449](https://github.com/nf-core/mhcquant/pull/449)
+- Sealed search-preset values: when a samplesheet row sets `SearchPreset`, preset values are no longer overridable via `--<param>`, `-params-file`, or `-c` for that row; rows without a preset resolve from `params` as before. Removed the fragile `workflow.commandLine` regex from `resolveSearchParams` (renamed to `resolvePresetParams`). Documented the new precedence in `docs/usage.md`. [#449](https://github.com/nf-core/mhcquant/pull/449)
 
 ### `Dependencies`
 
@@ -29,6 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | `MultiQC`  | 1.31.0      | 1.33.0      |
 | `Nf-core`  | 3.4.1       | 3.5.1       |
 | `openms`   | 3.4.1       | 3.5.0       |
+| `tdf2mzml` | 0.3.0       | 0.5.0       |
 
 ## 3.1.0 - BlüBa - 07/01/26
 

assets/multiqc_config.yml

@@ -3,7 +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/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>.
+  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/releases/tag/3.2.0" 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/3.2.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mhcquant-methods-description":
     order: -1000

assets/search_presets.tsv

@@ -1,11 +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)
+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)

conf/base.config

@@ -58,10 +58,10 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:NFCORE_MHCQUANT:MHCQUANT:PREPARE_SPECTRA:TDF2MZML {
-        cpus   = { 1     * task.attempt, 'cpus'   }
-        memory = { 10.GB * task.attempt, 'memory' }
-        time   = { 16.h  * task.attempt, 'time'   }
+    withName: 'TDF2MZML' {
+        cpus   = { 1     * task.attempt }
+        memory = { 10.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
     withName: 'PRIDEPY_FETCH_SDRF' {
         errorStrategy = 'retry'

conf/modules.config

@@ -273,37 +273,31 @@ process {
 }
 
 process {
-    if (params.quantify) {
-        withName: 'NFCORE_MHCQUANT:MHCQUANT:QUANT:OPENMS_IDSCORESWITCHER' {
-            ext.args   = [
-                "-new_score COMET:xcorr",
-                "-new_score_orientation higher_better",
-                "-old_score q-value"
-            ].join(' ').trim()
-            publishDir  = [
-                mode: params.publish_dir_mode,
-                pattern: '*.idXML',
-                enabled: false
-            ]
-        }
+    withName: 'NFCORE_MHCQUANT:MHCQUANT:QUANT:OPENMS_IDSCORESWITCHER' {
+        ext.args   = [
+            "-new_score COMET:xcorr",
+            "-new_score_orientation higher_better",
+            "-old_score q-value"
+        ].join(' ').trim()
+        publishDir  = [
+            mode: params.publish_dir_mode,
+            pattern: '*.idXML',
+            enabled: false
+        ]
     }
-}
 
-process {
-    if (params.rescoring_engine == 'mokapot') {
-        withName: 'NFCORE_MHCQUANT:MHCQUANT:RESCORE:OPENMS_IDSCORESWITCHER' {
-            ext.prefix  = {"${meta.id}"}
-            ext.args   = [
-                "-new_score q-value",
-                "-new_score_orientation lower_better",
-                "-old_score expect"
-            ].join(' ').trim()
-            publishDir  = [
-                mode: params.publish_dir_mode,
-                pattern: '*.idXML',
-                enabled: false
-            ]
-        }
+    withName: 'NFCORE_MHCQUANT:MHCQUANT:RESCORE:OPENMS_IDSCORESWITCHER' {
+        ext.prefix  = {"${meta.id}"}
+        ext.args   = [
+            "-new_score q-value",
+            "-new_score_orientation lower_better",
+            "-old_score expect"
+        ].join(' ').trim()
+        publishDir  = [
+            mode: params.publish_dir_mode,
+            pattern: '*.idXML',
+            enabled: false
+        ]
     }
 }
 
@@ -370,7 +364,7 @@ process {
     withName: 'OPENMS_IDMASSACCURACY' {
         ext.prefix  = {"${meta.spectra}"}
         ext.args    = { [
-            (params.precursor_error_units == 'ppm') ? "-precursor_error_ppm": "",
+            (meta.precursor_error_units == 'ppm') ? "-precursor_error_ppm": "",
             "-fragment_mass_tolerance ${meta.fragment_mass_tolerance}"
         ].join(' ').trim() }
         publishDir  = [
@@ -470,6 +464,7 @@ process {
     }
 
     withName: 'OPENMS_TEXTEXPORTER' {
+        ext.prefix  = { "${meta.id}_exported" }
         ext.args    = '-id:peptides_only -id:add_hit_metavalues 0 -id:add_metavalues 0'
         publishDir  = [
             enabled: false
@@ -546,19 +541,16 @@ process {
 }
 
 process {
-
-    if (params.annotate_ions) {
-        withName: 'PYOPENMS_IONANNOTATOR' {
-            ext.args   = { [
-                    "--precursor_charge ${meta.prec_charge}",
-                    "--fragment_mass_tolerance ${meta.fragment_mass_tolerance}",
-                    "--remove_precursor_peak ${params.remove_precursor_peak}"
-                ].join(' ').trim() }
-                publishDir  = [
-                    path: {"${params.outdir}/intermediate_results/ion_annotations"},
-                    mode: params.publish_dir_mode,
-                    pattern: '*.tsv'
-                ]
-        }
+    withName: 'PYOPENMS_IONANNOTATOR' {
+        ext.args   = { [
+            "--precursor_charge ${meta.prec_charge}",
+            "--fragment_mass_tolerance ${meta.fragment_mass_tolerance}",
+            "--remove_precursor_peak ${params.remove_precursor_peak}"
+        ].join(' ').trim() }
+        publishDir  = [
+            path: {"${params.outdir}/intermediate_results/ion_annotations"},
+            mode: params.publish_dir_mode,
+            pattern: '*.tsv'
+        ]
     }
 }

conf/test_single_quant.config

@@ -7,15 +7,18 @@
  *   nextflow run main.nf -profile test_single_quant,<docker/singularity>
  *  */
 
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test single replicate profile'
     config_profile_description = 'Test dataset to check pipeline function for single replicate'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input = params.pipelines_testdata_base_path + 'mhcquant/testdata/sample_sheet_single_quant.tsv'
 

docs/usage.md

@@ -90,13 +90,16 @@ ID	Sample	Condition	ReplicateFileName	SearchPreset
 
 ### Parameter precedence
 
-Search parameters are resolved with the following precedence (highest to lowest):
+When a samplesheet row sets `SearchPreset`, the preset's values are sealed in for that row's search — they cannot be overridden by `--<param>` on the CLI, by `-params-file`, or by `-c`. The following keys are sealed by the preset:
 
-1. **Command-line parameters** (e.g. `--fragment_mass_tolerance 0.05`) -- CLI overrides take highest priority and apply to all samples
-2. **Search preset** (e.g. `SearchPreset: lumos_class1`) -- preset values fill in any parameters not specified via CLI
-3. **Config defaults** (`nextflow.config`) -- built-in defaults are used as a final fallback
+`instrument`, `activation_method`, `digest_mass_range`, `prec_charge`, `precursor_mass_tolerance`, `precursor_error_units`, `fragment_mass_tolerance`, `fragment_bin_offset`, `number_mods`, `ms2pip_model`, `peptide_min_length`, `peptide_max_length`, `fixed_mods`, `variable_mods`.
 
-This means a CLI flag like `--fragment_mass_tolerance 0.05` will override all presets for that parameter.
+Rows that do **not** set `SearchPreset` resolve every key from the global Nextflow parameters (CLI > `-params-file` > `nextflow.config` defaults), exactly as in earlier releases.
+
+If you want to deviate from a built-in preset for a one-off run, either:
+
+1. Leave `SearchPreset` empty on the relevant rows and pass the values via `--<param>` / `-params-file` / a custom config; or
+2. Add a custom row to your own search-presets TSV (see `--search_presets`) and reference it by name from `SearchPreset`.
 
 > [!NOTE]
 > When using `--global_fdr`, samples sharing the same `SearchPreset` value are grouped together for global FDR estimation. Samples without a preset are grouped under a common `global` group.

modules.json

@@ -20,6 +20,11 @@
                         "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
+                    "openms/fileconverter": {
+                        "branch": "master",
+                        "git_sha": "924841ecdeb9b2aea108eda13cacf45a2452d35f",
+                        "installed_by": ["modules"]
+                    },
                     "openms/filefilter": {
                         "branch": "master",
                         "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
@@ -55,6 +60,11 @@
                         "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
+                    "openms/textexporter": {
+                        "branch": "master",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "installed_by": ["modules"]
+                    },
                     "openmsthirdparty/cometadapter": {
                         "branch": "master",
                         "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",

modules/local/openms/featurefinderidentification/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::openms=3.4.1
+  - bioconda::openms=3.5.0

modules/local/openms/featurefinderidentification/main.nf

@@ -4,8 +4,8 @@ process OPENMS_FEATUREFINDERIDENTIFICATION  {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
-        'biocontainers/openms:3.4.1--h81ffffe_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.5.0--h78fb946_0' :
+        'biocontainers/openms:3.5.0--h78fb946_0' }"
 
 
     input:

modules/local/openms/idconflictresolver/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::openms=3.4.1
+  - bioconda::openms=3.5.0

modules/local/openms/idconflictresolver/main.nf

@@ -4,8 +4,8 @@ process OPENMS_IDCONFLICTRESOLVER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
-        'biocontainers/openms:3.4.1--h81ffffe_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.5.0--h78fb946_0' :
+        'biocontainers/openms:3.5.0--h78fb946_0' }"
 
     input:
     tuple val(meta), path(consensus)

modules/local/openms/idmassaccuracy/main.nf

@@ -13,7 +13,7 @@ process OPENMS_IDMASSACCURACY {
     output:
     tuple val(meta), path("*frag_mass_err.tsv") , emit: frag_err
     tuple val(meta), path("*prec_mass_err.tsv") , emit: prec_err, optional: true
-	tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'"), topic: versions
+    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'"), topic: versions
 
     when:
     task.ext.when == null || task.ext.when