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Integrate cellsam - #10

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mikemcka wants to merge 15 commits into
WEHI-SODA-Hub:devfrom
mikemcka:integrate-cellsam
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Integrate cellsam#10
mikemcka wants to merge 15 commits into
WEHI-SODA-Hub:devfrom
mikemcka:integrate-cellsam

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@mikemcka

@mikemcka mikemcka commented Jan 9, 2026

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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
  • 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).

mikemcka and others added 15 commits January 6, 2026 14:54
@mikemcka
Add CellSAM segmentation integration
e70fb55 
- Add CellSAM as third segmentation option alongside Mesmer and Cellpose
- Implement CELLSAMSEGMENT module with OME-TIFF metadata parsing
- Add CELLSAM_SEGMENT and CELLSAM_SEGMENT_WBACKSUB subworkflows
- Support latest model weights (v1.2) via DEEPCELL_ACCESS_TOKEN
- Add configurable parameters for tiling and segmentation
- Include comprehensive tests and documentation
- Update README with CellSAM usage instructions
- Fix environment.yml files for cellmeasurement and combinechannels
@mikemcka
Add CellSAM parameters to nextflow schema for Sequera UI
6b948e0
@mikemcka
removed non-existant container line
fcacabe
@mikemcka
replaced readlink with direct file paths using PWD
a22471f
@mikemcka
fixed missing files for report issue
dfdc37f
@mikemcka
remove defaults channel
7c4acfc
@mikemcka
enable dask for parallelisation of tiling. increase requested time to…
38a5294 
… 48 hours
@mikemcka
fix dask beforescript
c9fd733
@mikemcka
fix config
142ed67
@mikemcka
fix time formats
90fd682
@mikemcka
update time request
e4df174
@mikemcka
update env to use new fork enabling dask
0af3a26
@mikemcka
revert back to non-parallelized workflow
9da84b8
@mikemcka
add wave container for cellsam
7446c91
@mikemcka
update readme
53f3a3e
@github-actions

github-actions Bot commented Jan 9, 2026

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This PR is against the main branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @mikemcka,

It looks like this pull-request is has been made against the mikemcka/sp_segment main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the mikemcka/sp_segment dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@mikemcka
mikemcka changed the base branch from main to dev January 9, 2026 02:57
@mikemcka
mikemcka changed the base branch from dev to main January 9, 2026 03:01
@mikemcka
mikemcka changed the base branch from main to dev January 12, 2026 01:12
@mikemcka mikemcka closed this Jan 23, 2026
@mikemcka
mikemcka deleted the integrate-cellsam branch January 23, 2026 00:03
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@mikemcka