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Merged
Parent: Release 1.1.0 - Resolution Road
merged 11 commits into from
Jan 5, 2024
Merged

Added anndata as an output format #49

merged 11 commits into from
Jan 5, 2024

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@FloWuenne
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@FloWuenne FloWuenne commented Jan 4, 2024 •
edited by kbestak
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PR checklist

This PR adds an additional output format downstream of spot2cell, namely data formatted in the anndata format as described in the squidpy tutorial: https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_read_spatial.html

Currently, the spot2cell data is reformatted to fit the anndata spatial requirements and then an anndata object is created. In the current version, the columns to remove from spot2cell are hardcoded.

This PR closes the #26.

  • 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/molkart branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core 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).

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github-actions bot commented Jan 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e095a69

+| ✅ 162 tests passed       |+
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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.

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-05 11:45:09

@kbestak kbestak self-requested a review January 5, 2024 11:51
kbestak
kbestak approved these changes Jan 5, 2024
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LGTM

@FloWuenne FloWuenne merged commit 252f68d into dev Jan 5, 2024
@FloWuenne FloWuenne deleted the anndata_output branch January 5, 2024 11:52
@FloWuenne FloWuenne mentioned this pull request Jan 5, 2024
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@kbestak kbestak kbestak approved these changes

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@FloWuenne @kbestak