Migrate to topic channels for versions #431

jonasscheid · 2026-01-08T16:29:23Z

Merge after #429

Nf-core module topic channel merge should be the next step. I did migrate to topic channels in pipeline nf-core modules for consistency reasons.

PR checklist

github-actions · 2026-01-08T16:31:16Z

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

Posted for pipeline commit d7a9324

+| ✅ 300 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
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
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/CONTRIBUTING.md
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/linting_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-mhcquant_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/images/nf-core-mhcquant_logo_light.png
files_exist - File found: docs/images/nf-core-mhcquant_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: assets/multiqc_config.yml
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-mhcquant_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/WorkflowMhcquant.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 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 ends in dev: 3.2.0dev
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.skip_decoy_generation= false
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.digest_mass_range= 800:2500
nextflow_config - Config default value correct: params.prec_charge= 2:3
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.use_x_ions= false
nextflow_config - Config default value correct: params.use_z_ions= false
nextflow_config - Config default value correct: params.use_a_ions= false
nextflow_config - Config default value correct: params.use_c_ions= false
nextflow_config - Config default value correct: params.use_NL_ions= false
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.version= false
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.plaintext_email= false
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.monochrome_logs= false
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/test_single_quant.nf.test' contains outdir parameter
nf_test_content - 'tests/test_single_quant.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_single_quant.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/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/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/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/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/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.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/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: 25.04.0, Config: 25.04.0
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: update-snapshots.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.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: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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 - OPENMS_FILECONVERTER 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-01-29 10:06:30

Updated CHANGELOG for version 3.2.0 with changes and dependency updates.

modules/local/openms/textexporter/main.nf

Copilot · 2026-01-09T08:35:24Z

@jonasscheid I've opened a new pull request, #433, to work on those changes. Once the pull request is ready, I'll request review from you.

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

Remove cache buster artifacts from topic channel migration

Joon-Klaps

Not 100% certain if everything went ok with template merge.

Think you might to fix of couple stuff first before the linter will be happy.

modules/local/easypqp/convert/main.nf

modules/local/openms/idconflictresolver/main.nf

modules/local/openms/mapaligneridentification/main.nf

modules/nf-core/openms/decoydatabase/main.nf

subworkflows/local/prepare_spectra/main.nf

subworkflows/local/quant/main.nf

subworkflows/local/rescore/main.nf

workflows/mhcquant.nf

…icated.

conf/modules.config

jonasscheid · 2026-01-28T16:11:14Z

@Joon-Klaps Thanks already for having a look! I updated every nf-core module to topics as well. Made the linter happy. Currently tests fail due to sever issue of a tool that we are dependent on. Should resolve itself after 1,2 tries. If you could have a look again, I would be grateful :)

EDIT: Seems to be a mqc issue. On it!

EDIT EDIT: Fixed 👍🏼

modules/local/openms/idconflictresolver/main.nf

Joon-Klaps

Think you still missed some stuff, mostly regarding the topics themselves

modules/local/openms/featurefinderidentification/main.nf

modules/local/openms/maprttransformer/main.nf

modules/local/openms/mztabexporter/main.nf

modules/local/openms/psmfeatureextractor/main.nf

modules/local/openms/textexporter/main.nf

subworkflows/local/rescore/main.nf

modules/local/openms/idmassaccuracy/main.nf

CHANGELOG.md

Co-authored-by: Joon Klaps <[email protected]>

subworkflows/local/rescore/main.nf

jonasscheid added 2 commits January 8, 2026 13:57

topic channel migration local modules

cb7bbb6

migrate nf-core modules,subworkflows to topic channels

3ceb970

jonasscheid requested a review from marissaDubbelaar as a code owner January 8, 2026 16:29

Add changelog entry for version 3.2.0

57c3e08

Updated CHANGELOG for version 3.2.0 with changes and dependency updates.

jonasscheid commented Jan 9, 2026

View reviewed changes

modules/local/openms/textexporter/main.nf Outdated Show resolved Hide resolved

Initial plan

5702f5e

Copilot AI mentioned this pull request Jan 9, 2026

Remove cache buster artifacts from topic channel migration #433

Merged

Copilot AI and others added 3 commits January 9, 2026 08:38

Remove all cache buster comments from local modules

ecd9f94

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

Merge pull request #433 from nf-core/copilot/sub-pr-431

9b7245a

Remove cache buster artifacts from topic channel migration

update snapshots with correct versions

f859ec4

jonasscheid changed the title ~~Migrate to topic channels~~ Migrate to topic channels for versions Jan 9, 2026

Joon-Klaps reviewed Jan 9, 2026

View reviewed changes

jonasscheid and others added 6 commits January 23, 2026 22:15

Merge branch 'dev' into topics

6ea4f5f

sync nf-core modules and bump openms version

81d9698

merge origin

8867477

port back nf-core to local: idmassaccuracy since module has been depr…

6defe0a

…icated.

update nf-core modules (with version topics)

a8ed2fa

rm idmassaccuracy from modules.json

20e9a0b

jonasscheid commented Jan 28, 2026

View reviewed changes

conf/modules.config Outdated Show resolved Hide resolved

jonasscheid commented Jan 28, 2026

View reviewed changes

conf/modules.config Outdated Show resolved Hide resolved

jonasscheid commented Jan 28, 2026

View reviewed changes

conf/modules.config Outdated Show resolved Hide resolved

jonasscheid commented Jan 28, 2026

View reviewed changes

conf/modules.config Outdated Show resolved Hide resolved

jonasscheid and others added 3 commits January 28, 2026 15:51

Apply suggestions from code review

04e7c58

fix typo

bd3903e

fix precommit

87ecb8b

jonasscheid added 2 commits January 29, 2026 07:35

Fix escaped backslash in idmassaccuracy version extraction

9e27576

Add OPENMS_IDMASSACCURACY to test snapshots

eb4b251

Update test_single_quant snapshot to 3.5.0 versions

859ae64

jonasscheid commented Jan 29, 2026

View reviewed changes

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Apply suggestion from @jonasscheid

6e8bd6e

Joon-Klaps reviewed Jan 29, 2026

View reviewed changes

jonasscheid and others added 7 commits January 29, 2026 09:35

Fix OpenMS tool formatting to use multi-line style

3b35783

Update CHANGELOG.md

91bb0f6

Co-authored-by: Joon Klaps <[email protected]>

Update subworkflows/local/rescore/main.nf

ae96114

Co-authored-by: Joon Klaps <[email protected]>

Update subworkflows/local/rescore/main.nf

8ba585a

Co-authored-by: Joon Klaps <[email protected]>

Update modules/local/openms/featurefinderidentification/main.nf

98fd653

Co-authored-by: Joon Klaps <[email protected]>

Update subworkflows/local/rescore/main.nf

17e6397

Co-authored-by: Joon Klaps <[email protected]>

Update subworkflows/local/prepare_spectra/main.nf

c767225

Co-authored-by: Joon Klaps <[email protected]>

nf-core deleted a comment from Joon-Klaps Jan 29, 2026

jonasscheid commented Jan 29, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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jonasscheid commented Jan 8, 2026 •

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

jonasscheid commented Jan 28, 2026 •

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