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new module pangolin/updatedata & patch pangolin/run #7182

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merged 8 commits into from
Dec 10, 2024

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Joon-Klaps
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@Joon-Klaps Joon-Klaps commented Dec 9, 2024

PR checklist

Creates a new module for pangolin for the sub-command --update-data. Moved previous pangolin to pangolin/run

  • 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

@Joon-Klaps Joon-Klaps changed the title new module pangolin-updatedataset new module pangolin/updatedataset Dec 9, 2024
@Joon-Klaps Joon-Klaps changed the title new module pangolin/updatedataset new module pangolin/updatedata & patch pangolin/run Dec 9, 2024
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Initially thought of making 2 PR's but because I had to rerun the snapshot I just updated both.

@Joon-Klaps Joon-Klaps marked this pull request as ready for review December 10, 2024 11:05
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@famosab famosab left a comment

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I would assert more than the name but other than that it looks good to me :)

@Joon-Klaps Joon-Klaps added this pull request to the merge queue Dec 10, 2024
Merged via the queue into master with commit 7860035 Dec 10, 2024
32 of 37 checks passed
@Joon-Klaps Joon-Klaps deleted the pangolin-updatedb branch December 10, 2024 14:50
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