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Implement singleR celltype annotation #44

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nictru
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@nictru nictru commented Jun 16, 2024

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@nictru nictru linked an issue Jun 16, 2024 that may be closed by this pull request
Implement SingleR cell type assignment #24
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github-actions bot commented Jun 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1419fa7

+| ✅ 196 tests passed       |+
!| ❗  16 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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: If applicable, make list of people who have also contributed
  • 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 README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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 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 2.14.1
  • Run at 2024-06-16 11:05:34

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nictru commented Jun 16, 2024 •
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Encountered a problem with the celldex R package, the functions are not available in the namespace as expected.

Reproduction:
docker run -it --entrypoint=R community.wave.seqera.io/library/anndata2ri_bioconductor-celldex_bioconductor-singlecellexperiment_bioconductor-singler_anndata:d6a21ee363999d21
library(celldex)
surveyReferences()

Result: Could not find function "surveyReferences"
Although this should be available according to the docs

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Implement SingleR cell type assignment
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