Feature oktoberfest by julianu · Pull Request #25 · nf-core/mspepid

julianu · 2026-08-27T15:43:01Z

This PR includes the Oktoberfest re-scoring into the pipeline - and several necessary enhancements to get it work as well as some fixes which accumulated. Apologies for the mix-up.

Some adjustments to mzML files, especially when created by Bruker, need to be performed as well.

PR checklist

github-actions · 2026-08-27T15:43:49Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

github-actions · 2026-08-27T15:49:41Z

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

Posted for pipeline commit 5bda6e6

+| ✅ 201 tests passed       |+
#| ❔   9 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  24 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in CHANGELOG.md: ## v1.0.0dev - [unreleased replace with date on release ]
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: # Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as output
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: .github/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
multiqc_config - multiqc_config

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/pr-comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-mspepid_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-mspepid_logo_light.png
files_exist - File found: docs/images/nf-core-mspepid_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-mspepid_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowMspepid.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
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: 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 (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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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 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 ends in dev: 1.0.0dev
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.entrapment_fold= 0
nextflow_config - Config default value correct: params.precursor_tol_ppm= 10
nextflow_config - Config default value correct: params.fragment_tol_da= 0.02
nextflow_config - Config default value correct: params.sage_prefilter= false
nextflow_config - Config default value correct: params.sage_prefilter_chunk_size= 0
nextflow_config - Config default value correct: params.run_comet= true
nextflow_config - Config default value correct: params.run_sage= true
nextflow_config - Config default value correct: params.run_percolator= true
nextflow_config - Config default value correct: params.run_ms2rescore= true
nextflow_config - Config default value correct: params.run_oktoberfest= true
nextflow_config - Config default value correct: params.ms2rescore_model= HCD
nextflow_config - Config default value correct: params.save_ms2rescore_model= false
nextflow_config - Config default value correct: params.oktoberfest_intensity_model= Prosit_2020_intensity_HCD
nextflow_config - Config default value correct: params.oktoberfest_irt_model= Prosit_2019_irt
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.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/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/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
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/pr-comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/nf-core-mspepid_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mspepid_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mspepid_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: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
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 - PSMUTILSCONVERSIONS found in conf/base.config and Nextflow scripts.
base_config - MS2RESCORE_RUNMS2RESCORE found in conf/base.config and Nextflow scripts.
base_config - OKTOBERFEST_RUNOKTOBERFEST 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 - TDF2MZML found in conf/modules.config and Nextflow scripts.
modules_config - ADJUSTMZML found in conf/modules.config and Nextflow scripts.
modules_config - PUBLISHMZML 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: 4.1.0
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 4.1.0
Run at 2026-09-04 07:10:57

github-actions · 2026-08-27T15:52:20Z

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

❌ docker | latest-everything | Shard 3/3

See the full run for details.

julianu added 21 commits September 2, 2026 10:46

starting with oktoberfest

cca0dd8

initial feature generation works

7c8d7e7

running oktoberfest

672e87b

adding test output

433855e

downgrade oktoberfest to 0.10.0 to make it work

57d0c9e

rename to runoktoberfest

95c285a

fixing small oktoberfest settings

6ef8adc

adding required adjustment of mzML files

d3034f1

label is annotated explicitly

c392cd2

use pass-through module for mzml publishing

ce3e3af

parameterization of oktoberfest models

ceb0cc4

allow override of used koina server

48b3d2d

updateing test results and parameters

0c9d943

updateing documentation

cbe1b0d

changing oktoberfest image due to date error

f17352c

do not automatically publish the ms2rescore model

ff81b5d

deactivate ms2rescoring and oktoberfest in minimal test

d7f9a1c

fixing small issue which never leaves a loop correctly

dfc1272

fixing probelm with spectra names containing multiple dots in the name

7c4c85f

provide a clear error on wron e and p values before log transformation

3860abb

fixing problems with the passing of versions

6cd1297

julianu force-pushed the feature_oktoberfest branch from 562a092 to 6cd1297 Compare September 2, 2026 10:47

julianu requested a review from di-hardt September 2, 2026 10:56

julianu added 2 commits September 2, 2026 14:56

updates to use Oktoberfest v0.11.1

a5490f0

adding citation

5bda6e6

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Feature oktoberfest - #25

Feature oktoberfest#25
julianu wants to merge 23 commits into
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feature_oktoberfest

julianu commented Aug 27, 2026 •

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❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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github-actions Bot commented Aug 27, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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❌ nf-test failed with latest Nextflow version

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julianu commented Aug 27, 2026 •

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

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