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PCA integration method implemented + tested#265

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nictru merged 21 commits intonf-core:devfrom
gregothebyteknight:dev
Apr 11, 2026
Merged

PCA integration method implemented + tested#265
nictru merged 21 commits intonf-core:devfrom
gregothebyteknight:dev

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@gregothebyteknight gregothebyteknight commented Mar 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 nf-core/scdownstream 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).

kim-fehl and others added 3 commits March 11, 2026 19:03
add pca integration method and align embedding handling
fbf9be2 
- add pca to integration methods (schema/docs/cellxgene list)
wire SCANPY_PCA into INTEGRATE and publish outputs
- use X_emb for PCA in integrated AnnData for downstream consistency
fix(scanpy): align pca module image with pipeline scanpy stack
c674e5e
@gregothebyteknight
Add PCA link to README.md
ea18649
nictru
nictru reviewed Mar 12, 2026
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Comment thread nf-test.config Outdated
nictru
nictru requested changes Mar 12, 2026
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Looks good so far! Can you just create a dedicated test in the INTEGRATE subworkflow?

nictru
nictru reviewed Mar 13, 2026
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Comment thread modules/local/scarches/expimap/environment.yml Outdated
Comment thread modules/local/scanpy/pca/environment.yml Outdated
Comment thread modules/local/scarches/expimap/templates/expimap.py Outdated
@nictru nictru linked an issue Apr 8, 2026 that may be closed by this pull request
Allow processing data with PCA instead of actual integration #179
Closed
@nictru
Merge remote-tracking branch 'origin/dev' into gregothebyteknight/dev
54a6c54 
Made-with: Cursor

# Conflicts:
#	CITATIONS.md
#	modules/local/scanpy/pca/environment.yml
#	modules/local/scanpy/pca/main.nf
#	nextflow_schema.json
@nictru nictru linked an issue Apr 10, 2026 that may be closed by this pull request
Add ExpiMap integration method #246
Closed
@nictru nictru merged commit b8aeaf2 into nf-core:dev Apr 11, 2026
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Add ExpiMap integration method Allow processing data with PCA instead of actual integration

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@gregothebyteknight @kim-fehl @nictru