remove consensusid and move to parquet by daichengxin · Pull Request #708 · bigbio/quantms

daichengxin · 2026-06-06T03:24:19Z

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qodo-code-review · 2026-06-06T03:24:23Z

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coderabbitai · 2026-06-06T03:24:26Z

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codacy-production · 2026-06-06T03:24:46Z

Not up to standards ⛔

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Nf core template merge 4.0.2 2

update onsite

Copilot

Pull request overview

This PR updates the quantms Nextflow pipeline to remove the legacy ConsensusID-based path and standardize identification artifacts around the .idparquet format, while also syncing multiple nf-core/module/template and CI components (Nextflow + nf-core tooling + nf-test).

Changes:

Refactors the TMT isobaric workflow to use a new ISOBARIC_WORKFLOW module and routes quant outputs through parquet-compatible steps.
Migrates multiple ID-processing steps/modules from idXML to idparquet and removes deprecated modules/subworkflows (ConsensusID, IsobaricAnalyzer-based feature mapper/protein inference/protein quant, etc.).
Updates testing and automation: nf-test workflow addition, MultiQC module update, nf-schema plugin bump, Nextflow minimum version bump, and CI/lint workflow changes.

Reviewed changes

Copilot reviewed 113 out of 116 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
workflows/tmt.nf	Switches TMT path to `ISOBARIC_WORKFLOW` + `MSSTATS_CONVERTER` and updates emitted outputs
workflows/quantms.nf	Minor formatting adjustments in versions topic aggregation
tests/default.nf.test	Adjusts snapshot inputs to separate stable path vs stable content
subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config	Bumps nf-schema plugin version used in tests
subworkflows/nf-core/utils_nfschema_plugin/main.nf	Improves help handling when `--help true` is passed
subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap	Adds snapshot for new nf-test coverage
subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test	Adds nf-test for `UTILS_NFCORE_PIPELINE`
subworkflows/nf-core/utils_nfcore_pipeline/main.nf	Adjusts `emit:` and removes IM notification helper
subworkflows/local/utils_nfcore_quantms_pipeline/main.nf	Removes hook_url / imNotification wiring from completion workflow
subworkflows/local/protein_quant/meta.yml	Removes deprecated local protein quant subworkflow metadata
subworkflows/local/protein_quant/main.nf	Removes deprecated local protein quant subworkflow implementation
subworkflows/local/protein_inference/meta.yml	Removes deprecated local protein inference subworkflow metadata
subworkflows/local/protein_inference/main.nf	Removes deprecated local protein inference subworkflow implementation
subworkflows/local/phospho_scoring/main.nf	Simplifies PTM localization path to always run ONSITE directly
subworkflows/local/peptide_database_search/main.nf	Reworks rescoring/fine-tuning sampling and switches cleaning to parquet outputs
subworkflows/local/feature_mapper/meta.yml	Removes deprecated feature mapper subworkflow metadata
subworkflows/local/feature_mapper/main.nf	Removes deprecated feature mapper subworkflow implementation
subworkflows/local/dda_id/main.nf	Simplifies DDA ID-only workflow; removes PSM conversion step
ro-crate-metadata.json	Updates RO-Crate metadata (dates, Nextflow minimum, attribution fields)
README.md	Updates Nextflow badge/version and fixes nf-core documentation links
nextflow.config	Adds/changes onsite params, bumps Nextflow min version, adjusts publishDir compatibility, removes hook_url
nextflow_schema.json	Syncs schema with new onsite params and defaults (e.g., `lfq_seeding_algorithm`) and removes hook_url
modules/nf-core/multiqc/tests/nextflow.config	Adjusts MultiQC test args (`-p`)
modules/nf-core/multiqc/tests/main.nf.test.snap	Updates MultiQC snapshots for new outputs (including parquet)
modules/nf-core/multiqc/tests/main.nf.test	Refactors MultiQC module tests for tuple/meta-based IO
modules/nf-core/multiqc/meta.yml	Updates module schema to tuple/meta IO and adds container lock metadata
modules/nf-core/multiqc/main.nf	Updates MultiQC module to tuple/meta IO and emits versions as tuples (not versions.yml)
modules/nf-core/multiqc/environment.yml	Bumps MultiQC conda version to 1.34
modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt	Adds arm64 conda lockfile for MultiQC 1.34
modules/local/utils/spectrum_features/meta.yml	Updates expected ID file patterns to `.idparquet`
modules/local/utils/spectrum_features/main.nf	Updates rescoring container and switches CLI to `--idparquet`
modules/local/utils/psm_conversion/meta.yml	Removes deprecated PSM conversion module metadata
modules/local/utils/psm_conversion/main.nf	Removes deprecated PSM conversion module implementation
modules/local/utils/psm_clean/meta.yml	Updates expected ID file patterns to `.idparquet`
modules/local/utils/psm_clean/main.nf	Updates rescoring container and outputs `.idparquet` clean IDs
modules/local/utils/msrescore_fine_tuning/meta.yml	Updates expected ID file patterns to `.idparquet`
modules/local/utils/msrescore_fine_tuning/main.nf	Updates rescoring container and switches CLI to `--idparquet`/list handling
modules/local/utils/msrescore_features/meta.yml	Updates expected ID file patterns to `.idparquet`
modules/local/utils/msrescore_features/main.nf	Updates rescoring container tag/version
modules/local/openms/sage/meta.yml	Updates Sage output pattern to `.idparquet`
modules/local/openms/sage/main.nf	Pins OpenMS thirdparty container version tag
modules/local/openms/proteomicslfq/meta.yml	Updates ProteomicsLFQ input pattern to `.idparquet`
modules/local/openms/proteomicslfq/main.nf	Pins container tag and updates debug outputs to `.idparquet` naming
modules/local/openms/protein_quantifier/meta.yml	Removes deprecated ProteinQuantifier module metadata
modules/local/openms/protein_quantifier/main.nf	Removes deprecated ProteinQuantifier module implementation
modules/local/openms/protein_inference_generic/meta.yml	Removes deprecated ProteinInference module metadata
modules/local/openms/protein_inference_generic/main.nf	Removes deprecated ProteinInference module implementation
modules/local/openms/protein_inference_epifany/meta.yml	Removes deprecated Epifany module metadata
modules/local/openms/protein_inference_epifany/main.nf	Removes deprecated Epifany module implementation
modules/local/openms/percolator/meta.yml	Updates Percolator input pattern to `.idparquet`
modules/local/openms/percolator/main.nf	Pins OpenMS thirdparty container version tag
modules/local/openms/msgf/meta.yml	Updates MSGF output pattern to `.idparquet`
modules/local/openms/msgf/main.nf	Pins OpenMS thirdparty container version tag
modules/local/openms/isobaric_workflow/meta.yml	Adds new OpenMS `IsobaricWorkflow` module metadata
modules/local/openms/isobaric_workflow/main.nf	Adds new OpenMS `IsobaricWorkflow` process implementation
modules/local/openms/isobaric_analyzer/meta.yml	Removes deprecated IsobaricAnalyzer module metadata
modules/local/openms/isobaric_analyzer/main.nf	Removes deprecated IsobaricAnalyzer module implementation
modules/local/openms/index_peptides/meta.yml	Updates PeptideIndexer IO patterns to `.idparquet`
modules/local/openms/index_peptides/main.nf	Updates PeptideIndexer output extension to `.idparquet`
modules/local/openms/id_score_switcher/meta.yml	Removes deprecated IDScoreSwitcher module metadata
modules/local/openms/id_score_switcher/main.nf	Removes deprecated IDScoreSwitcher module implementation
modules/local/openms/id_mapper/meta.yml	Removes deprecated IDMapper module metadata
modules/local/openms/id_mapper/main.nf	Removes deprecated IDMapper module implementation
modules/local/openms/id_filter/main.nf	Updates tag logic to reflect `.idparquet` suffix handling
modules/local/openms/id_conflict_resolver/meta.yml	Removes deprecated IDConflictResolver module metadata
modules/local/openms/id_conflict_resolver/main.nf	Removes deprecated IDConflictResolver module implementation
modules/local/openms/generate_decoy_database/main.nf	Pins OpenMS thirdparty container version tag
modules/local/openms/false_discovery_rate/meta.yml	Removes deprecated FalseDiscoveryRate module metadata
modules/local/openms/false_discovery_rate/main.nf	Removes deprecated FalseDiscoveryRate module implementation
modules/local/openms/extractfeatures/main.nf	Removes deprecated `PSMFeatureExtractor` wrapper module
modules/local/openms/consensusid/meta.yml	Removes ConsensusID module metadata
modules/local/openms/consensusid/main.nf	Removes ConsensusID module implementation
modules/local/openms/comet/meta.yml	Updates Comet output pattern to `.idparquet`
modules/local/openms/comet/main.nf	Pins OpenMS thirdparty container version tag
modules/bigbio/onsite/tests/main.nf.test.snap	Adds snapshots for updated onsite module tests
modules/bigbio/onsite/tests/main.nf.test	Updates onsite tests to use idparquet inputs/outputs and tagging
modules/bigbio/onsite/meta.yml	Updates module schema to tuple/meta IO and idparquet patterns
modules/bigbio/onsite/main.nf	Updates onsite container, switches to idparquet IO, extends params support
modules/bigbio/onsite/environment.yml	Bumps pyonsite to 0.0.4 and updates env schema header
modules.json	Updates module/subworkflow git SHAs to match updated installs
main.nf	Removes `hook_url` argument from completion subworkflow call
docs/usage.md	Expands/updates onsite parameter documentation
docs/CONTRIBUTING.md	Adds contributing guide under docs and links from template/README
conf/tests/test_localize.config	Adds onsite tuning params for localization CI profile
conf/modules/shared.config	Extends publishDir selector to include `ISOBARIC_WORKFLOW`
conf/modules/id.config	Removes ConsensusID config and updates ID_FILTER suffixes to `.idparquet`
conf/dev.config	Pins dev containers for OpenMS thirdparty and pyonsite
conf/base.config	Adjusts default retry exit codes and revises resource labels/defaults
CITATIONS.md	Formatting tweak in MultiQC citation blockquote
assets/tmt18plex_default_correction.matrix	Formatting normalization (no content change)
assets/slackreport.json	Removes Slack notification template asset
assets/multiqc_config.yml	Updates pmultiqc ID pattern from `.idXML` to `.idparquet`
assets/adaptivecard.json	Removes MS Teams adaptive card template asset
AGENTS.md	Updates examples to refer to `.idparquet` patterns
.vscode/settings.json	Adds tracked VS Code markdown styling setting
.prettierignore	Stops ignoring removed notification templates
.pre-commit-config.yaml	Updates prettier version, narrows excludes, and adds nextflow-lint hook
.nf-core.yml	Bumps nf-core tools version to 4.0.2
.gitignore	Simplifies ignore list and adds `.lineage/`
.github/workflows/template-version-comment.yml	Updates pinned action SHAs and doc link
.github/workflows/release-announcements.yml	Adds release-toot/Bluesky announcement workflow
.github/workflows/nf-test.yml	Adds dedicated nf-test workflow with sharding and profiles
.github/workflows/linting.yml	Updates linting workflow to use prek/uv and new action pins
.github/workflows/linting_comment.yml	Updates pinned action SHAs
.github/workflows/fix_linting.yml	Updates to use prek and nf-core bot token for pushing fixes
.github/workflows/extended_ci.yml	Bumps Nextflow version and matrix handling for exec profiles
.github/workflows/download_pipeline.yml	Adds workflow to test `nf-core pipelines download` behavior
.github/workflows/clean-up.yml	Updates pinned stale action SHA
.github/workflows/ci.yml	Bumps Nextflow version in CI matrix
.github/workflows/branch.yml	Updates pinned action SHA
.github/PULL_REQUEST_TEMPLATE.md	Updates contributing links and dataset repo reference
.github/actions/nf-test/action.yml	Updates action versions/pins for setup tools
.github/actions/get-shards/action.yml	Updates setup-nf-test action pin

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+    PERCOLATOR(ch_id_files_feats)
+    ch_rescoring_results = PERCOLATOR.out.id_files_perc
+    ch_software_versions = ch_software_versions.mix(PERCOLATOR.out.versions)


                        .combine(ch_mzmls_search, by: 0)
                        .toSortedList()
                        .flatMap()
                        .randomSample(params.fine_tuning_sample_run, 2025)
-                        .combine(channel.value("sage"))
                        .groupTuple(by: 3)


    output:
-    tuple val(meta), path("${id_file.baseName}_*.idXML"), emit: ptm_in_id_onsite
+    tuple val(meta), path("${prefix}_*.idparquet"), emit: ptm_in_id_onsite
    path "versions.yml", emit: versions


    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
-        onsite: \$(onsite --version 2>&1 | grep -oP 'version \\K[0-9.]+' || echo "unknown")
+        onsite: \$(onsite --version 2>&1 | grep -oE 'version \\K[0-9.]+' || echo "unknown")


      - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
        env:
          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md


+        fragment_unit = params.onsite_fragment_error_units ?: 'Da'
+        def optional_flags = [add_decoys, compute_all_scores, debug].findAll { a -> a }.join(' \\\n            ')
        algorithm_cmd = """


+        fragment_unit = params.onsite_fragment_error_units ?: 'Da'
+        def optional_flags = [add_decoys, compute_all_scores, debug].findAll { a -> a }.join(' \\\n            ')


jpfeuffer · 2026-06-18T14:17:22Z

haha shouldnt we do the review BEFORE merging?
Are you going to follow up on the issues?

jpfeuffer · 2026-06-18T14:17:33Z

But really nice. I will test this soon.

daichengxin added 2 commits June 6, 2026 11:20

Merge pull request #88 from bigbio/dev

cbd9547

Dev

remove consensusid and move to parquet

0dccd6e

daichengxin added 8 commits June 6, 2026 11:37

update

59e9461

Update main.nf

3f76281

Update main.nf

3566881

update

acf43d2

bump

3d233db

update

d451d98

update TMT

e2839a8

Update main.nf

2f6e1c5

This was linked to issues Jun 6, 2026

Implement qpx as output for both TMT and LFQ #705

Open

Discussion: replace ConsensusID with a more robust multi-engine rescoring path #707

Open

daichengxin mentioned this pull request Jun 6, 2026

Major refactoring in the Isobaric workflow enabling to work similar to proteomicsLFQ #692

Draft

11 tasks

daichengxin and others added 14 commits June 6, 2026 16:55

Update main.nf

1edb72a

update

82d2f5d

update

5d1dc3d

update onsite

1980e0a

update

584222e

Update modules.json

423393f

Update modules.json

cab3755

Template update for nf-core/tools version 4.0.2

22245f4

Template update for nf-core/tools version 4.0.2

5eef337

Template update for nf-core/tools version 4.0.2

e149f25

Template update for nf-core/tools version 4.0.2

cdaa38b

Template update for nf-core/tools version 4.0.2

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Template update for nf-core/tools version 4.0.2

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addd

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daichengxin added 19 commits June 14, 2026 23:08

remove

8d4b017

update

c3f0a76

update onsite

e362145

Update usage.md

f36eebc

Update test_localize.config

9dc4380

Merge pull request #89 from daichengxin/nf-core-template-merge-4.0.2-2

95c295f

Nf core template merge 4.0.2 2

update onsite

647fe38

Update main.nf

763c00f

Merge pull request #90 from daichengxin/nf-core-template-merge-4.0.2-2

d4b7c72

update onsite

Update test_localize.config

430256c

Update extended_ci.yml

2aadc5d

Update extended_ci.yml

7531c97

test

eebe255

update

b6d005d

Update main.nf

a5b40c3

fixed bugs

48ddb9a

Update test_localize.config

a3aac43

fixed bugs

47416d7

recover ci

3feaa3e

daichengxin requested a review from ypriverol June 18, 2026 06:05

daichengxin added 2 commits June 18, 2026 14:39

Update dev.config

dff5d4e

rename

8f00555

daichengxin linked an issue Jun 18, 2026 that may be closed by this pull request

Support the new biosaour for MBR as default quant method in proteomicsLFQ #704

Open

ypriverol requested a review from Copilot June 18, 2026 13:38

ypriverol approved these changes Jun 18, 2026

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ypriverol merged commit 5147de0 into bigbio:dev Jun 18, 2026
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remove consensusid and move to parquet#708

remove consensusid and move to parquet#708
ypriverol merged 52 commits into
bigbio:devfrom
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		fragment_unit = params.onsite_fragment_error_units ?: 'Da'
		def optional_flags = [add_decoys, compute_all_scores, debug].findAll { a -> a }.join(' \\\n ')

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daichengxin commented Jun 6, 2026

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