Release 3.1.0 #401

jonasscheid · 2025-09-17T13:17:43Z

`Added`

Added a peptidoform column to the pipeline output #376
Added Boxplot of intensity distributions to the MulitQC report #382
Added a config option to hide outliers in box plots, add plot descriptions #387
Added a Fasta column to the input samplesheet to enable sample-specific FASTA files #391

`Fixed`

Fixed an issue with not providing the full process name in conf/base.config #384
Template update 3.1.1, migrate to nf-test #379
Fixed the binning of the TICs histogram and move the general stats table to the top of the report #388
Write out FDR-filtered peptide list in global FDR-mode, instead of 100% FDR list #394
Update labels for global FDR process configurations #397

`Dependencies`

Dependency	Old version	New version
`MultiQC`	1.28.0	1.30.0
`Nf-core`	3.2.1	3.3.2
`EasyPQP`	0.1.51	0.1.53

PR checklist

Co-authored-by: Maxime U Garcia <[email protected]>

…hcquant into template-merge-331

…nsistencies

Add box plots to the MulitQC report

Added '--diannpqp' argument to ext.args in two configurations.

Updated MS2rescore container

Bump easypqp and enable diann2-compatible output

Update labels for global FDR process configurations

Co-authored-by: jonasscheid <[email protected]>

…examples Co-authored-by: jonasscheid <[email protected]>

Co-authored-by: jonasscheid <[email protected]>

…b49-09177a236da5 Update documentation with new subworkflows and global FDR mode

Co-authored-by: axelwalter <[email protected]>

github-actions · 2025-09-17T13:19:42Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 08479da

+| ✅ 295 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: CHANGELOG.md
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files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
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nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: validation.help.enabled
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version does not contain dev for release: 3.1.0
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.run_centroidisation= false
nextflow_config - Config default value correct: params.pick_ms_levels= 2
nextflow_config - Config default value correct: params.filter_mzml= false
nextflow_config - Config default value correct: params.instrument= high_res
nextflow_config - Config default value correct: params.enzyme= unspecific cleavage
nextflow_config - Config default value correct: params.activation_method= ALL
nextflow_config - Config default value correct: params.precursor_mass_tolerance= 5
nextflow_config - Config default value correct: params.precursor_error_units= ppm
nextflow_config - Config default value correct: params.fragment_bin_offset= 0.0
nextflow_config - Config default value correct: params.fragment_mass_tolerance= 0.01
nextflow_config - Config default value correct: params.number_mods= 3
nextflow_config - Config default value correct: params.variable_mods= Oxidation (M)
nextflow_config - Config default value correct: params.num_hits= 1
nextflow_config - Config default value correct: params.remove_precursor_peak= false
nextflow_config - Config default value correct: params.spectrum_batch_size= 0
nextflow_config - Config default value correct: params.rescoring_engine= percolator
nextflow_config - Config default value correct: params.feature_generators= deeplc,ms2pip
nextflow_config - Config default value correct: params.ms2pip_model= Immuno-HCD
nextflow_config - Config default value correct: params.deeplc_calibration_set_size= 0.15
nextflow_config - Config default value correct: params.fdr_level= peptide_level_fdrs
nextflow_config - Config default value correct: params.fdr_threshold= 0.01
nextflow_config - Config default value correct: params.global_fdr= false
nextflow_config - Config default value correct: params.subset_max_train= 0
nextflow_config - Config default value correct: params.quantify= false
nextflow_config - Config default value correct: params.max_rt_alignment_shift= 300
nextflow_config - Config default value correct: params.quantification_min_prob= 0.0
nextflow_config - Config default value correct: params.quantification_mz_window= 5.0
nextflow_config - Config default value correct: params.quantification_rt_window= 0.0
nextflow_config - Config default value correct: params.quantification_mapping_tolerance= 0.0
nextflow_config - Config default value correct: params.quantification_peak_width= 60.0
nextflow_config - Config default value correct: params.quantification_min_peak_width= 0.2
nextflow_config - Config default value correct: params.peptide_min_length= 8
nextflow_config - Config default value correct: params.peptide_max_length= 12
nextflow_config - Config default value correct: params.generate_speclib= false
nextflow_config - Config default value correct: params.annotate_ions= false
nextflow_config - Config default value correct: params.epicore= false
nextflow_config - Config default value correct: params.epicore_min_overlap= 11
nextflow_config - Config default value correct: params.epicore_max_step_size= 5
nextflow_config - Config default value correct: params.epicore_min_epi_length= 11
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nf_test_content - 'tests/mokapot.nf.test' contains outdir parameter
nf_test_content - 'tests/mokapot.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mokapot.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/epicore.nf.test' contains outdir parameter
nf_test_content - 'tests/epicore.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/epicore.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/speclib.nf.test' contains outdir parameter
nf_test_content - 'tests/speclib.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/speclib.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/ionannotator.nf.test' contains outdir parameter
nf_test_content - 'tests/ionannotator.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/ionannotator.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
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files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
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files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
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files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-mhcquant_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mhcquant_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mhcquant_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.10.5, Config: 24.10.5
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - NFCORE_MHCQUANT found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - THERMORAWFILEPARSER found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - UNZIP found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_FILEFILTER found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_DECOYDATABASE found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_PEAKPICKERHIRES found in conf/modules.config and Nextflow scripts.
modules_config - OPENMSTHIRDPARTY_COMETADAPTER found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_PEPTIDEINDEXER found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDMERGER found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDMERGER_GLOBAL found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDFILTER_Q_VALUE found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDFILTER_Q_VALUE_GLOBAL found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDFILTER_GLOBAL found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDFILTER_FOR_SPECLIB found in conf/modules.config and Nextflow scripts.
modules_config - EASYPQP_CONVERT found in conf/modules.config and Nextflow scripts.
modules_config - EASYPQP_LIBRARY found in conf/modules.config and Nextflow scripts.
modules_config - EASYPQP_LIBRARY_GLOBAL found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDFILTER_QUANT found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDRIPPER found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_MHCQUANT found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_MHCQUANT found in conf/modules.config and Nextflow scripts.
modules_config - TDF2MZML found in conf/modules.config and Nextflow scripts.
modules_config - PYOPENMS_CHROMATOGRAMEXTRACTOR found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_MAPALIGNERIDENTIFICATION found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_MAPRTTRANSFORMERMZML found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDMASSACCURACY found in conf/modules.config and Nextflow scripts.
modules_config - MS2RESCORE found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_PERCOLATORADAPTER found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_PERCOLATORADAPTER_GLOBAL found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_PSMFEATUREEXTRACTOR found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_MZTABEXPORTER found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_FEATUREFINDERIDENTIFICATION found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_FEATURELINKERUNLABELEDKD found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_TEXTEXPORTER found in conf/modules.config and Nextflow scripts.
modules_config - SUMMARIZE_RESULTS found in conf/modules.config and Nextflow scripts.
modules_config - EPICORE found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_TEXTEXPORTER_GLOBAL found in conf/modules.config and Nextflow scripts.
modules_config - OPENMS_IDCONFLICTRESOLVER found in conf/modules.config and Nextflow scripts.
modules_config - PYOPENMS_IONANNOTATOR found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 3.1.0, nfcore_yml.version = 3.1.0
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.3.2
Run at 2025-09-24 11:16:09

Update docs

Add unique_accessions column and remove special character '#' from the OpenMS TextExporter output

JuliaGraf and others added 30 commits May 26, 2025 16:36

Add proteoform to pipeline output

6611217

Update changelog

3cfc6f0

Lint Changelog

f1a4385

Merge pull request #376 from JuliaGraf/proteoform

d332972

Template update for nf-core/tools version 3.3.1

18a2222

initial commit

aae99a1

merge template

110bcef

add default snap

9c4bf03

fix ro-crate-metadata

ebfce73

fix maintainers

5dd26cf

fix some nf-core linting warnings and bump mqc version

7b9212c

fix default nf-test

c2447d4

fix trailing whitespace

2ce1816

nf-test.yml aktualisieren

e2702e7

Co-authored-by: Maxime U Garcia <[email protected]>

fix pyopenms version parsing, update snapshot

1f041cf

Merge branch 'template-merge-331' of https://github.com/jonasscheid/m…

2d657df

…hcquant into template-merge-331

Put result file temporarily on ignore list due to float rounding inco…

6cceff2

…nsistencies

Put result file temporarily on ignore list due to float rounding inco…

b05cd9f

…nsistencies

add mqc_length_dist file to ignore list

cc7dcdf

update snapshot

1f5f47f

Change lineplots to box plots

fc16d95

Add peptide intensity box plots

21873d1

Change to log2

abb9ae5

Update assets/multiqc_config.yml

c9478b5

Update CHANGELOG.md

adc185f

Merge pull request #382 from JuliaGraf/boxplots

b56ca9f

Add box plots to the MulitQC report

Round all float values to 5 decimals to ensure stable checksums

a47b375

Merge branch 'dev' into template-merge-331

19f5607

Update base.config

61b50f5

Update CHANGELOG.md

7fd77ef

jonasscheid and others added 22 commits September 11, 2025 15:59

Update easypqp container version to 0.1.53

9847879

Add '--diannpqp' argument to module configurations

3644224

Added '--diannpqp' argument to ext.args in two configurations.

Update easypqp version to 0.1.53 in tests

c36f52b

Merge branch 'nf-core:dev' into dev

7977a34

Update EasyPQP version in CHANGELOG

d2b018e

Merge pull request #395 from steffenlem/dev

ac3e51f

Updated MS2rescore container

Merge pull request #396 from nf-core/bump-easypqp

2e4e215

Bump easypqp and enable diann2-compatible output

Update labels for global configurations

0796acf

Add high memory and CPU processing configuration

8206507

Fix changelog entry for FDR-filtered peptide list

57b9436

Merge pull request #397 from nf-core/fix-globalfdr-ressource_allocation

deda148

Update labels for global FDR process configurations

Initial plan

20e4ba8

Update README with new subworkflows and global FDR documentation

552ee83

Co-authored-by: jonasscheid <[email protected]>

Update usage documentation with new subworkflows and features

7a9b2d5

Co-authored-by: jonasscheid <[email protected]>

Address reviewer feedback: restructure documentation and consolidate …

a547bd0

…examples Co-authored-by: jonasscheid <[email protected]>

Remove mokapot from complete workflow example

42cf58e

Co-authored-by: jonasscheid <[email protected]>

Merge pull request #399 from nf-core/copilot/fix-72f40d13-378b-4ce8-b…

c8bc8ab

…b49-09177a236da5 Update documentation with new subworkflows and global FDR mode

lint

ed63780

sync ro crate

5205b44

Update README.md

0aed628

Co-authored-by: axelwalter <[email protected]>

Update docs/usage.md

fbc0e1d

Co-authored-by: axelwalter <[email protected]>

Update docs/usage.md

1cdd1f5

Co-authored-by: axelwalter <[email protected]>

jonasscheid and others added 7 commits September 17, 2025 14:11

fix linting

da6155a

update snapshots with release version

9f7c2a5

Merge pull request #400 from nf-core/update-docs

2d30adf

Update docs

Add a column for unique accessions

9368daa

Remove special character from column name to resolve bug

80c5a3a

Update changelog

527305b

Merge pull request #403 from JuliaGraf/unique_accessions

08479da

Add unique_accessions column and remove special character '#' from the OpenMS TextExporter output

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Release 3.1.0 #401

Release 3.1.0 #401

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jonasscheid commented Sep 17, 2025

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github-actions bot commented Sep 17, 2025 •

edited

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Release 3.1.0 #401

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Release 3.1.0 #401

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jonasscheid commented Sep 17, 2025

Added

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github-actions bot commented Sep 17, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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`Added`

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github-actions bot commented Sep 17, 2025 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️