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5127 new module xenium ranger #6826

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5127 new module xenium ranger #6826

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@khersameesh24 khersameesh24 commented Oct 22, 2024 •
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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

Sameesh Kher and others added 14 commits May 17, 2024 16:37
Initial commit for the xeniumranger module
9ec866c
test file correction, placeholder code for relabel
ae9bc52
minor fix for segmentation input for xenium import-segmentation
631481c
test cases for xenium modules
fe10e6a
changes in test config, minor fixes for dockerfile versioning, test s…
e2a05e2 
…uite changes,readme update
updated container image for xeniumranger
8294642
@khersameesh24
Updated xeniumranger version hence the dockerfile, added newer submod…
fee6db0 
…ule for xeniumranger rename
@khersameesh24
Updated xeniumranger version hence the dockerfile, added newer submod…
54a02a8 
…ule for xeniumranger rename
@khersameesh24
testing xenium modules, tests for rename module
79ed3ba
minor fixes for relabel
9fff425
fix for outs directory
bf94049
minor fixes for resegment
147e3b3
tested xeniumranger modules with test data, fixed nf-test, testdata f…
bb1893b 
…etch
fixed linting issues with xenium modules
f407f0d
@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
new module: Xenium Ranger #5127
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@khersameesh24 khersameesh24 self-assigned this Oct 26, 2024
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@mashehu mashehu mashehu left review comments

@vagkaratzas vagkaratzas Awaiting requested review from vagkaratzas vagkaratzas was automatically assigned from nf-core/nf-test

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot adamrtalbot is a code owner automatically assigned from nf-core/a-team

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@khersameesh24 khersameesh24

Labels
new module Adding a new module Ready for Review ready to merge
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Hackathon October 2024
Status: Done
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new module: Xenium Ranger
3 participants
@khersameesh24 @mashehu @Tobiaspk