Release 1.8.0 - Major changes with quantms-rescoring, openms, qpx by daichengxin · Pull Request #710 · bigbio/quantms

daichengxin · 2026-06-23T08:29:57Z

PR checklist

Dev

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

…tion Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Bump version to new release cycle. Add SDRF agent skill

…tandard Enable ext.args support in GENERATE_CFG module

strict syntax

…nput Deprecate OpenMS experimental design format, enforce SDRF-only input

remove consensusid and move to parquet

update onsite

qodo-code-review · 2026-06-23T08:30:02Z

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coderabbitai · 2026-06-23T08:30:10Z

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📥 Commits

Reviewing files that changed from the base of the PR and between e719f43 and 606bac0.

⛔ Files ignored due to path filters (14)

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📒 Files selected for processing (189)

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.github/actions/nf-test/action.yml
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github-actions · 2026-06-23T08:34:07Z

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

Posted for pipeline commit 606bac0

+| ✅ 117 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   9 tests had warnings |!

Details

❗ Test warnings:

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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
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_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/lint_results.md: _* pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/dda_id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
_
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/lint_results.md: _* pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
_
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/dda_id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
_
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
_

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: conf/test.config
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/ci.yml
files_exist - File is ignored: .github/workflows/download_pipeline.yml
files_exist - File is ignored: .github/workflows/nf-test.yml
files_exist - File is ignored: .gitignore
files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: conf/igenomes_ignored.config
nextflow_config - nextflow_config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/quantms/quantms/.github/workflows/awstest.yml
multiqc_config - multiqc_config
modules_config - modules_config

✅ Tests passed:

files_exist - File found: .gitattributes
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/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-quantms_logo_light.png
files_exist - File found: docs/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-quantms_logo_light.png
files_exist - File found: docs/images/nf-core-quantms_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: 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-quantms_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/WorkflowQuantms.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
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 - 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/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 - .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
readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
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: nf-test.yml
actions_schema_validation - Workflow validation passed: extended_ci.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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.
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: 4.0.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 1.8.0, nfcore_yml.version = 1.8.0
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 4.0.2
Run at 2026-06-24 12:37:16

…d psm_fdr_control; update dda_id and id subworkflows

…images

Copilot

Pull request overview

Release 1.8.0 updates the quantms Nextflow pipeline to a new processing model (parquet-centric / updated OpenMS tooling), removes DIA-NN + MSstats post-processing from the codebase, and refreshes nf-core template and CI/linting to newer versions.

Changes:

Refactor LFQ/TMT workflows to use updated OpenMS components (e.g., IsobaricWorkflow, QPX outputs) and parquet-based ID handling.
Remove DIA-NN workflow + MSstats post-processing modules/scripts; update configs, docs, and citations accordingly.
Update nf-core template components (MultiQC, schema plugin, utils), test datasets URLs, and CI/linting tooling.

Reviewed changes

Copilot reviewed 188 out of 202 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
workflows/tmt.nf	Refactor TMT workflow to IsobaricWorkflow + converter
workflows/lfq.nf	Remove MSstats post step; adjust versions + outputs
tests/nextflow.config	Point tests to bigbio/quantms-test-datasets
tests/default.nf.test	Snapshot inputs renamed (stable path vs content)
subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config	Bump nf-schema plugin version
subworkflows/nf-core/utils_nfschema_plugin/main.nf	Avoid treating `--help true` as help string
subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap	Add snapshot for utils_nfcore_pipeline tests
subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test	Add nf-test coverage for utils_nfcore_pipeline
subworkflows/nf-core/utils_nfcore_pipeline/main.nf	Fix emit syntax; remove IM notification helper
subworkflows/local/utils_nfcore_quantms_pipeline/main.nf	Remove hook_url notification; add removed-param guard
subworkflows/local/psm_rescoring/main.nf	Simplify rescoring to per-file Percolator only
subworkflows/local/psm_fdr_control/meta.yml	Remove obsolete subworkflow metadata
subworkflows/local/psm_fdr_control/main.nf	Remove obsolete PSM FDR control subworkflow
subworkflows/local/protein_quant/meta.yml	Remove obsolete protein quant subworkflow metadata
subworkflows/local/protein_quant/main.nf	Remove obsolete protein quant subworkflow
subworkflows/local/protein_inference/meta.yml	Remove obsolete protein inference metadata
subworkflows/local/protein_inference/main.nf	Remove obsolete protein inference subworkflow
subworkflows/local/phospho_scoring/main.nf	Simplify onsite call; remove score switching branch
subworkflows/local/input_check/meta.yml	Remove `is_sdrf` output from contract
subworkflows/local/input_check/main.nf	Treat all inputs as SDRF; delegate to samplesheet_check
subworkflows/local/id/meta.yml	Remove consensusid/psm_fdr_control components
subworkflows/local/id/main.nf	Remove ConsensusID/PSM_FDR_CONTROL path; wire to rescoring
subworkflows/local/file_preparation/main.nf	Improve .d handling, optional stats, Nextflow 26 style
subworkflows/local/feature_mapper/meta.yml	Remove obsolete subworkflow metadata
subworkflows/local/feature_mapper/main.nf	Remove obsolete feature mapper subworkflow
subworkflows/local/dda_id/meta.yml	Update declared components (remove removed steps)
subworkflows/local/create_input_channel/meta.yml	Remove DIA channel output from contract
modules/nf-core/multiqc/tests/nextflow.config	Set MultiQC args for tests
modules/nf-core/multiqc/main.nf	Update MultiQC container/version + tuple IO changes
modules/nf-core/multiqc/environment.yml	Bump MultiQC conda package to 1.34
modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap	Remove deprecated module tests snapshot
modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test	Remove deprecated module tests
modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py	Remove deprecated module template
modules/nf-core/custom/dumpsoftwareversions/meta.yml	Remove deprecated module metadata
modules/nf-core/custom/dumpsoftwareversions/main.nf	Remove deprecated dumpsoftwareversions module
modules/nf-core/custom/dumpsoftwareversions/environment.yml	Remove deprecated module env
modules/local/utils/tdf2mzml/main.nf	Improve rename logic; pass args; avoid same-file rename
modules/local/utils/spectrum_features/meta.yml	Update ID format to idparquet
modules/local/utils/spectrum_features/main.nf	Update quantms-rescoring image + idparquet interface
modules/local/utils/psm_conversion/meta.yml	Remove obsolete psm conversion module metadata
modules/local/utils/psm_conversion/main.nf	Remove obsolete psm conversion module
modules/local/utils/psm_clean/meta.yml	Update ID format to idparquet
modules/local/utils/psm_clean/main.nf	Update container + idparquet interface (cleaning)
modules/local/utils/mzml_statistics/main.nf	Bump quantms-utils; pass ext.args
modules/local/utils/msrescore_fine_tuning/meta.yml	Update ID format to idparquet
modules/local/utils/msrescore_fine_tuning/main.nf	Update container + idparquet interface (fine tuning)
modules/local/utils/msrescore_features/meta.yml	Update ID format to idparquet
modules/local/utils/msrescore_features/main.nf	Update container + idparquet interface (features)
modules/local/utils/extract_sample/meta.yml	Remove obsolete extract sample module metadata
modules/local/utils/extract_sample/main.nf	Remove obsolete extract sample module
modules/local/utils/decompress_dotd/main.nf	Fix executor check; chmod fix; robust .d rename
modules/local/samplesheet_check/meta.yml	Update input/output patterns for SDRF normalization
modules/local/samplesheet_check/main.nf	Normalize to *.sdrf.tsv; CSV->TSV conversion; add args
modules/local/preprocess_expdesign/main.nf	Bump quantms-utils container
modules/local/openms/sage/meta.yml	Update output to idparquet
modules/local/openms/sage/main.nf	Update OpenMS image + idparquet output; cleanup
modules/local/openms/proteomicslfq/meta.yml	Update ID input to idparquet; remove triqler output
modules/local/openms/proteomicslfq/main.nf	Add qpx output; add seeding algorithm param; idparquet
modules/local/openms/protein_quantifier/meta.yml	Remove obsolete protein_quantifier module metadata
modules/local/openms/protein_quantifier/main.nf	Remove obsolete protein_quantifier module
modules/local/openms/protein_inference_generic/meta.yml	Remove obsolete protein inference module metadata
modules/local/openms/protein_inference_generic/main.nf	Remove obsolete protein inference module
modules/local/openms/protein_inference_epifany/meta.yml	Remove obsolete epifany module metadata
modules/local/openms/protein_inference_epifany/main.nf	Remove obsolete epifany module
modules/local/openms/percolator/meta.yml	Update input ID format to idparquet
modules/local/openms/percolator/main.nf	Update OpenMS image + idparquet output; set score:fdr
modules/local/openms/openms_peak_picker/main.nf	Fix `inmemory` option typo
modules/local/openms/mzml_indexing/main.nf	Pass ext.args into FileConverter
modules/local/openms/msgf/meta.yml	Update output ID format to idparquet
modules/local/openms/msgf/main.nf	Update OpenMS image + idparquet output; env detection
modules/local/openms/luciphor/meta.yml	Remove obsolete luciphor module metadata
modules/local/openms/luciphor/main.nf	Remove obsolete luciphor module
modules/local/openms/isobaric_workflow/meta.yml	Add new module metadata (currently malformed)
modules/local/openms/isobaric_workflow/main.nf	New IsobaricWorkflow module wrapper
modules/local/openms/isobaric_analyzer/meta.yml	Remove obsolete isobaric_analyzer metadata
modules/local/openms/isobaric_analyzer/main.nf	Remove obsolete isobaric_analyzer module
modules/local/openms/index_peptides/meta.yml	Update ID format to idparquet
modules/local/openms/index_peptides/main.nf	Update output ID format to idparquet
modules/local/openms/id_score_switcher/meta.yml	Remove obsolete id_score_switcher metadata
modules/local/openms/id_score_switcher/main.nf	Remove obsolete id_score_switcher module
modules/local/openms/id_ripper/meta.yml	Remove obsolete id_ripper metadata
modules/local/openms/id_ripper/main.nf	Remove obsolete id_ripper module
modules/local/openms/id_merger/main.nf	Update merged output to idparquet; simplify prefix logic
modules/local/openms/id_mapper/meta.yml	Remove obsolete id_mapper metadata
modules/local/openms/id_mapper/main.nf	Remove obsolete id_mapper module
modules/local/openms/id_filter/meta.yml	Remove obsolete id_filter metadata
modules/local/openms/id_filter/main.nf	Remove obsolete id_filter module
modules/local/openms/id_conflict_resolver/meta.yml	Remove obsolete conflict resolver metadata
modules/local/openms/id_conflict_resolver/main.nf	Remove obsolete conflict resolver module
modules/local/openms/generate_decoy_database/main.nf	Update OpenMS image version
modules/local/openms/false_discovery_rate/meta.yml	Remove obsolete FDR module metadata
modules/local/openms/false_discovery_rate/main.nf	Remove obsolete FDR module
modules/local/openms/consensusid/meta.yml	Remove obsolete consensusid metadata
modules/local/openms/consensusid/main.nf	Remove obsolete consensusid module
modules/local/openms/comet/meta.yml	Update output ID format to idparquet
modules/local/openms/comet/main.nf	Update OpenMS image; idparquet output; simplify iso range
modules/local/msstats/msstats_tmt/meta.yml	Remove MSstatsTMT module metadata
modules/local/msstats/msstats_tmt/main.nf	Remove MSstatsTMT process
modules/local/msstats/msstats_lfq/meta.yml	Remove MSstats module metadata
modules/local/msstats/msstats_lfq/main.nf	Remove MSstats LFQ process
modules/local/diann/preliminary_analysis/meta.yml	Remove DIA-NN module metadata
modules/local/diann/preliminary_analysis/main.nf	Remove DIA-NN process
modules/local/diann/insilico_library_generation/meta.yml	Remove DIA-NN module metadata
modules/local/diann/insilico_library_generation/main.nf	Remove DIA-NN process
modules/local/diann/individual_analysis/meta.yml	Remove DIA-NN module metadata
modules/local/diann/individual_analysis/main.nf	Remove DIA-NN process
modules/local/diann/generate_cfg/meta.yml	Remove DIA-NN config generator metadata
modules/local/diann/generate_cfg/main.nf	Remove DIA-NN config generator process
modules/local/diann/final_quantification/meta.yml	Remove DIA-NN final quant metadata
modules/local/diann/final_quantification/main.nf	Remove DIA-NN final quant process
modules/local/diann/convert_results/meta.yml	Remove DIA-NN conversion metadata
modules/local/diann/convert_results/main.nf	Remove DIA-NN conversion process
modules/local/diann/assemble_empirical_library/meta.yml	Remove DIA-NN library assembly metadata
modules/local/diann/assemble_empirical_library/main.nf	Remove DIA-NN library assembly process
modules/bigbio/thermorawfileparser/thermorawfileparser.diff	Patch applied to upstream bigbio module
modules/bigbio/thermorawfileparser/tests/main.nf.test.snap	Update snapshots for patched module
modules/bigbio/thermorawfileparser/tests/main.nf.test	Update tests for new outputs/topics
modules/bigbio/thermorawfileparser/meta.yml	Update module metadata to nf-core schema style
modules/bigbio/thermorawfileparser/main.nf	Update IO + versions topic; adjust stub/output naming
modules/bigbio/thermorawfileparser/environment.yml	Remove `name:` key from conda env
modules/bigbio/onsite/tests/main.nf.test.snap	Add onsite module snapshots
modules/bigbio/onsite/meta.yml	Update onsite metadata schema + idparquet support
modules/bigbio/onsite/environment.yml	Bump pyonsite to 0.0.5
modules.json	Update pinned module SHAs + apply thermoraw patch
main.nf	Remove hook_url from completion workflow inputs
docs/usage.md	Document SDRF-only input + new onsite params
conf/tests/test_localize.config	Update onsite params + remove MSstats skip flag
conf/tests/test_lfq.config	Switch LFQ test input to SDRF-only; remove obsolete params
conf/tests/test_lfq_sage.config	Remove redundant tolerances/params
conf/tests/test_latest_dia.config	Remove DIA test profile
conf/tests/test_full_tmt.config	Switch full TMT testdata URLs to bigbio repo
conf/tests/test_full_lfq.config	Switch full LFQ testdata URLs; remove triqler
conf/tests/test_full_dia.config	Remove DIA full test profile
conf/tests/test_dia.config	Remove DIA test profile
conf/modules/verbose_modules.config	Remove publishDir blocks for removed modules
conf/modules/tmt.config	Add TMT-specific config (selector currently mismatched)
conf/modules/shared.config	Add shared publishDir for SDRF + quant tables + stats
conf/modules/lfq.config	Add LFQ-specific ext.args config
conf/modules/id.config	Add ID/PSM ext.args config (onsite/percolator/msrescore)
conf/dev.config	Update OpenMS and onsite container images
conf/base.config	Update retry exit statuses; adjust label resource defaults
CITATIONS.md	Remove DIA-NN/Triqler citations; formatting tweak
CHANGELOG.md	Add 1.8.0 release notes + breaking changes
bin/msstats_utils.R	Remove MSstats helper R script
assets/tmt18plex_default_correction.matrix	Reformat file with consistent indentation
assets/slackreport.json	Remove Slack notification template
assets/multiqc_config.yml	Update release link + idparquet glob
assets/adaptivecard.json	Remove Teams adaptive card template
.vscode/settings.json	Add VSCode markdown style setting
.prettierignore	Remove deleted JSON templates; ignore agent/skill files
.pre-commit-config.yaml	Bump prettier; adjust excludes; add nextflow-lint hook
.nf-core.yml	Update nf-core template version + pipeline version
.gitignore	Replace older ignores with `.lineage/` ignore
.github/workflows/template-version-comment.yml	Update action pins + docs link
.github/workflows/release-announcements.yml	Add Mastodon/Bluesky release announcements
.github/workflows/linting.yml	Switch to prek + uv; update action pins (has a logic bug)
.github/workflows/linting_comment.yml	Update action pins
.github/workflows/fix_linting.yml	Switch fix-linting to prek + Nextflow setup
.github/workflows/extended_ci.yml	Bump Nextflow; drop DIA profiles; matrix exec_profile
.github/workflows/diann_private.yml	Remove fork-specific DIA workflow
.github/workflows/clean-up.yml	Update action pin
.github/workflows/ci.yml	Bump Nextflow; drop DIA profile
.github/workflows/branch.yml	Update add-pr-comment action pin
.github/PULL_REQUEST_TEMPLATE.md	Fix CONTRIBUTING link path
.github/actions/nf-test/action.yml	Update setup-nextflow/setup-nf-test/setup-apptainer pins
.github/actions/get-shards/action.yml	Update setup-nf-test pin

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daichengxin and others added 30 commits January 12, 2026 09:54

Merge pull request #83 from bigbio/dev

645f7a5

Dev

Initial plan

ab543df

Deprecate OpenMS experimental design format and simplify input handling

c891fdb

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Update CHANGELOG to clarify breaking change for OpenMS format depreca…

d894bae

…tion Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Remove unnecessary is_sdrf parameter from CREATE_INPUT_CHANNEL

c3eb44d

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Update nextflow_schema.json

38deb26

Move OpenMS deprecation to version 1.8.0 as requested

5e523a3

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Initial plan

b313dbc

Add ext.args support to GENERATE_CFG module

bcef6d7

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Bump version to new release cycle. Add SDRF agent skill

3ee699c

ignores

4e7ad8f

Update ro-crate-metadata.json

a1ed80f

wth

2a9640a

Update input URL for LFQ test configuration

85c44df

Merge pull request #643 from bigbio/newrelcycle

f7757ba

Bump version to new release cycle. Add SDRF agent skill

Merge pull request #641 from bigbio/copilot/update-ext-args-nf-core-s…

1cee707

…tandard Enable ext.args support in GENERATE_CFG module

fixes?

bf27b7f

is_sdrf

cfdfc5d

Merge branch 'dev' into copilot/deprecate-openms-schema-input

8f41ca5

significant cleanup and strict syntax review

bbe8fcc

more

d94897b

fix fix linting wf

76048f8

fix args

e6b324d

Merge pull request #644 from bigbio/strict_syntax

cc20b80

strict syntax

Merge branch 'dev' into copilot/deprecate-openms-schema-input

822b7cb

precommit

79d2170

fix???

8886fe0

Include inputs in SDRF TSV output path

77a7320

Update input file format from CSV to TSV

5f22aa8

Merge pull request #639 from bigbio/copilot/deprecate-openms-schema-i…

eeae581

…nput Deprecate OpenMS experimental design format, enforce SDRF-only input

daichengxin and others added 13 commits June 15, 2026 20:28

test

eebe255

update

b6d005d

Update main.nf

a5b40c3

fixed bugs

48ddb9a

Update test_localize.config

a3aac43

fixed bugs

47416d7

recover ci

3feaa3e

Update dev.config

dff5d4e

rename

8f00555

Merge pull request #708 from daichengxin/dev

5147de0

remove consensusid and move to parquet

update onsite

ce64d34

Update dev.config

7b139a2

Merge pull request #709 from daichengxin/dev

4e33a0e

update onsite

daichengxin added 5 commits June 23, 2026 16:53

Update CHANGELOG for 1.8.0 release

196b5e0

Bump version from 1.8.0dev to 1.8.0 for release

75524f6

Enable nf-core custom config include

8c7e650

Update module configs: id, shared, tmt, verbose; cleanup id_filter an…

42466ba

…d psm_fdr_control; update dda_id and id subworkflows

Remove PSM_FDR_CONTROL import from dda_id subworkflow

5446848

ypriverol self-requested a review June 23, 2026 12:05

ypriverol approved these changes Jun 23, 2026

View reviewed changes

daichengxin added 2 commits June 24, 2026 10:07

Update docs/images: remove DIA-LFQ from quantms.svg, clean up unused …

d70657e

…images

Fix trailing whitespace in SVG files

cb84e43

ypriverol requested a review from Copilot June 24, 2026 08:43

Copilot started reviewing on behalf of ypriverol June 24, 2026 08:44 View session

Copilot AI reviewed Jun 24, 2026

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Update tmt.config, msstats_converter and isobaric_workflow meta

606bac0

ypriverol merged commit 149493c into master Jun 24, 2026
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Release 1.8.0 - Major changes with quantms-rescoring, openms, qpx#710

Release 1.8.0 - Major changes with quantms-rescoring, openms, qpx#710
ypriverol merged 205 commits into
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daichengxin commented Jun 23, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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coderabbitai Bot commented Jun 23, 2026 •

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