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New module: anndata/getsize module #6925

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merged 8 commits into from
Nov 11, 2024

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LeonHafner
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@LeonHafner LeonHafner commented Nov 2, 2024

Adding the module anndata/getsize which outputs the size of an anndata object.
This can then be used to add the size of the anndata object to its meta map:
ANNDATA_GETSIZE.out.size.map{meta, txt -> [meta, txt.text.toInteger()]}

Currently there is no proper H5AD data on the test-datasets modules branch. For now I used the files from the scdownstream pipeline, but I will try to add proper test data to the modules asap.

PR checklist

Closes #6923

  • 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

@LeonHafner LeonHafner added new module Adding a new module draft labels Nov 2, 2024
@LeonHafner LeonHafner self-assigned this Nov 2, 2024
@LeonHafner LeonHafner removed the draft label Nov 2, 2024
@LeonHafner LeonHafner marked this pull request as ready for review November 2, 2024 19:06
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@SPPearce SPPearce left a comment

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Generally fine.
It would be good to put a h5ad file into the modules test-datasets though, are you able to do that?

@LeonHafner LeonHafner requested a review from SPPearce November 9, 2024 12:08
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@SPPearce SPPearce left a comment

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Looks good to me now, thanks for putting the file into the modules testdata repo.

Co-authored-by: Simon Pearce <[email protected]>
@LeonHafner LeonHafner enabled auto-merge November 11, 2024 09:20
@LeonHafner LeonHafner added this pull request to the merge queue Nov 11, 2024
Merged via the queue into nf-core:master with commit 685fbea Nov 11, 2024
13 of 15 checks passed
@LeonHafner LeonHafner deleted the anndata_getsize branch November 11, 2024 09:33
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new module: anndata/getsize
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