Skip to content

bump openms version 3.6.0 - #736

Merged
jpfeuffer merged 3 commits into
bigbio:devfrom
daichengxin:dev
Oct 5, 2026
Merged

bump openms version 3.6.0#736
jpfeuffer merged 3 commits into
bigbio:devfrom
daichengxin:dev

Conversation

@daichengxin

@daichengxin daichengxin commented Oct 1, 2026

Copy link
Copy Markdown
Collaborator

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the bigbio/quantms branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@qodo-code-review

qodo-code-review Bot commented Oct 1, 2026

Copy link
Copy Markdown
Contributor

ⓘ Qodo reviews are paused because the subscription is no longer active. Ask your workspace admin to reactivate the subscription to resume reviews. Manage billing

@coderabbitai

coderabbitai Bot commented Oct 1, 2026 •
edited
Loading

Copy link
Copy Markdown
Contributor

Important

Review skipped

Auto reviews are disabled on base/target branches other than the default branch.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration
  • Configuration used: defaults
  • Review profile: CHILL
  • Plan: Advanced
  • Run ID: 04fc77bf-07b1-4f06-8fcb-e8e9e801df8a

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

  • 🔍 Trigger review
  • Autopilot · Keep fixing CodeRabbit findings and required CI, and resolving merge conflicts

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

Comment @coderabbitai help to get the list of available commands.

@daichengxin daichengxin linked an issue Oct 1, 2026 that may be closed by this pull request
Segfault in QTClusterFinder/FeatureGroupingAlgorithmQT during ProteomicsLFQ cross-run alignment with Sage identifications #735
Open
@github-actions

github-actions Bot commented Oct 1, 2026 •
edited
Loading

Copy link
Copy Markdown

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a93daa2

+| ✅ 117 tests passed       |+
#| ❔  18 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   7 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 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_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • 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:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-04 07:38:24

@daichengxin daichengxin mentioned this pull request Oct 1, 2026
Closed
@jpfeuffer

jpfeuffer commented Oct 1, 2026

Copy link
Copy Markdown
Collaborator

Nice. Ill check the error. By the way with the right configuration, OpenMS should be able to read Thermo Raw and Bruker .d natively. Also Percolator has been natively integrated. Maybe we can simplify the workflow with this.
Not sure what was enabled in the docker container @timosachsenberg

@jpfeuffer jpfeuffer mentioned this pull request Oct 1, 2026
Merged
timosachsenberg pushed a commit to OpenMS/OpenMS that referenced this pull request Oct 1, 2026
@jpfeuffer
[FIX] MSGF+ features: set NaN fragment error stdevs to 0 for Percolat…
be727ad 
…or (#10382)

MS-GF+ computes the -addFeatures fragment error standard deviations as
sqrt(E[x^2] - mean^2) in single precision; with identical fragment errors
the variance rounds below 0 and MS-GF+ writes "NaN". Since #10314 the
in-process PercolatorAdapter rejects non-finite features, which broke the
quantms TMT tests with OpenMS 3.6.0 (bigbio/quantms#736). The variance is
~0, so addMSGFFeatures now sets these features to 0.

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
@jpfeuffer

jpfeuffer commented Oct 5, 2026

Copy link
Copy Markdown
Collaborator

looks good. let's merge?

@jpfeuffer
jpfeuffer merged commit 1cc9a50 into bigbio:dev Oct 5, 2026
38 of 39 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@jpfeuffer jpfeuffer jpfeuffer approved these changes

Assignees

No one assigned

Labels

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

Segfault in QTClusterFinder/FeatureGroupingAlgorithmQT during ProteomicsLFQ cross-run alignment with Sage identifications

3 participants

@daichengxin @jpfeuffer @ypriverol