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5127 new module xenium ranger #6826

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@khersameesh24 khersameesh24 commented Oct 22, 2024

PR checklist

Closes #XXX

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@khersameesh24 khersameesh24 requested a review from a team as a code owner October 22, 2024 14:07
@khersameesh24 khersameesh24 requested review from vagkaratzas and removed request for a team October 22, 2024 14:07
@mashehu mashehu changed the base branch from 5127-new-module-xenium-ranger to master October 22, 2024 14:10
@mashehu mashehu requested a review from a team as a code owner October 22, 2024 14:10
@khersameesh24 khersameesh24 linked an issue Oct 22, 2024 that may be closed by this pull request
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@khersameesh24 khersameesh24 self-assigned this Oct 26, 2024
Comment on lines 8 to 15
val(meta)
path(xenium_bundle)
val(expansion_distance)
path(coordinate_transform)
path(nuclei)
path(cells)
path(transcript_assignment)
path(viz_polygons)
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Sample specific data should go in the same tuple as meta.
Reference data should either go in one tuple with it's own meta or in separate channels per datatype, again each with it's own meta

example: https://github.com/nf-core/modules/blob/master/modules/nf-core/snapaligner/align/main.nf#L10

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Code Changed -> Tested -> Updated PR ✌🏻

Comment on lines 8 to 15
val(meta)
path(xenium_bundle)
val(expansion_distance)
path(coordinate_transform)
path(nuclei)
path(cells)
path(transcript_assignment)
path(viz_polygons)
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path(viz_polygons)

output:
tuple val(meta), path("**/outs/**"), emit: outs
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What does the tool output? different file formats should also have different output channels

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Hi Matthias, the output for xeniumranger modules is reupdated in the input files just like other 10x tools, multiple files are updated for every run and hence we do not have a dedicated channel for the outputs

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new module: Xenium Ranger
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