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Dev#83

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daichengxin merged 33 commits intodaichengxin:devfrom
bigbio:dev
Jan 12, 2026
Merged

Dev#83
daichengxin merged 33 commits intodaichengxin:devfrom
bigbio:dev

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@daichengxin daichengxin commented Jan 12, 2026

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).

weizhongchun and others added 30 commits December 30, 2025 16:28
@weizhongchun
using the bigbio onsite module
cc3f895
@weizhongchun
some changes
928a835
@weizhongchun
pre-commit
d262ece
@weizhongchun
some changes
e69769c
@ypriverol
Merge pull request #631 from daichengxin/dev
4659730 
fixed quantms-rescoring
@ypriverol
Merge branch 'dev' into dev
cd6cd05
@ypriverol
Update modules/bigbio/onsite/main.nf
a379a92 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@ypriverol
Remove 'openms' label from ONSITE process
0f9b061
@ypriverol
Merge pull request #630 from weizhongchun/dev
6130dc6 
using the bigbio onsite module
@ypriverol @coderabbitai
Update subworkflows/local/peptide_database_search/main.nf
60f5ee6 
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
@daichengxin
refine
2bd3823
@weizhongchun
fix some issues
9eccd24
@weizhongchun
update git_sha
2a5ac6c
@ypriverol
Merge pull request #634 from weizhongchun/dev
ef6f0dd 
Fix some issues in onsite
@daichengxin
update changlog and figure
438ecad
@daichengxin
Update quantms_metro.drawio.svg
e398af5
@daichengxin
Update quantms_metro.drawio.svg
2444953
@daichengxin
Update quantms_metro.drawio.svg
c469992
@ypriverol @qodo-code-review
Update assets/multiqc_config.yml
56db5be 
Co-authored-by: qodo-code-review[bot] <151058649+qodo-code-review[bot]@users.noreply.github.com>
@ypriverol
remove info in favor of warn
8c94daa
@ypriverol
changes in CHANGELOG
c962bc7
@ypriverol
Changes in CHANGELOG
3f6c085
@ypriverol
change CHANGELOG.md
3539f7d
@ypriverol
minor change
2f52c34
@ypriverol
Merge pull request #635 from ypriverol/dev
5b69680 
small changes for release
@jpfeuffer @coderabbitai
Update nextflow_schema.json
7d53f46 
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
@jpfeuffer
Update minimum probability description in JSON schema
97cf63a
@ypriverol
minor changes for release
c82a165
@ypriverol
Merge pull request #636 from ypriverol/dev
609bb8b 
minor changes for release
@ypriverol
last change
36bcf1c
ypriverol and others added 3 commits January 8, 2026 22:59
@daichengxin daichengxin merged commit 645f7a5 into daichengxin:dev Jan 12, 2026
27 checks passed
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4 participants

@daichengxin @weizhongchun @ypriverol @jpfeuffer