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Visium HD support

Open cavenel opened this issue 1 year ago • 7 comments

This PR adds support for Visium HD slides.

  • [ ] Update metro map with Visium HD

cavenel avatar Dec 20 '24 13:12 cavenel

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit d664714

+| ✅ 218 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   6 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

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  • 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.
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  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

:grey_question: Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-09-05 13:44:22

github-actions[bot] avatar Dec 20 '24 13:12 github-actions[bot]

[!WARNING] Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1. Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

nf-core-bot avatar Jan 10 '25 13:01 nf-core-bot

On the Visium HD flag, wouldn't it be more convenient using the slide serial number prefix to determine Visium version instead of requiring a dedicated flag? Prefixes are defined here, would be "H1" for current version of Visium HD.

sebotic avatar Jan 29 '25 23:01 sebotic

On the Visium HD flag, wouldn't it be more convenient using the slide serial number prefix to determine Visium version instead of requiring a dedicated flag? Prefixes are defined here, would be "H1" for current version of Visium HD.

So you mean that we remove the --visium_hd flag, and instead rely on the first one or two characters of the slide column in the input csv? That's an option indeed. But if we take the first two digits, then the pipeline won't work when 10X starts making H2, even if they keep backward compatibility. What would be the best approach? @fasterius do you have an opinion on this?

cavenel avatar Jan 31 '25 08:01 cavenel

If we can read the correct parameters from the samplesheet that's great, as long as it doesn't introduce issues with misidentifying anything. Regarding backwards compatibility, why wouldn't the pipeline work anymore when 10X starts making H2? If we're matching for H1 we can also match for H2 or HN, no?

fasterius avatar Jan 31 '25 08:01 fasterius

If we're matching for H1 we can also match for H2 or HN, no?

Definitely, I was more thinking that it means updating the pipeline at each new version, but that's probably needed anyway to update SR versions etc. So yes sounds like a good idea to check Visium version from slide id!

cavenel avatar Jan 31 '25 08:01 cavenel

I now removed the --visium_hd flag in https://github.com/nf-core/spatialvi/pull/101/commits/dd9a8ba2cd6e13bda1d6e0f63655fd4b896cda1f For downstream analysis, as we do not give "slide" parameter, I use the existence of a "binned_outputs" folder in the SpaceRanger output.

cavenel avatar Feb 07 '25 13:02 cavenel