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Add sylph/profile module #7118

Merged
merged 64 commits into from
Jan 30, 2025
Merged

Add sylph/profile module #7118

merged 64 commits into from
Jan 30, 2025

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sofstam
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@sofstam sofstam commented Nov 28, 2024

PR checklist

Moves the local module sylph/profile to nf-core modules. Closes nf-core/seqinspector#65
Removes unnecessary pattern from sylph/sketch meta file.

  • 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

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@famosab famosab left a comment

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Suggested to be a bit more specific about the created csv :)

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@SPPearce
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SPPearce commented Jan 8, 2025

@sofstam , do you need a hand to get this finished off?

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sofstam commented Jan 8, 2025

@SPPearce Was on holidays, looking at the comments now :)

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sofstam commented Jan 24, 2025

@famosab The tests are passing now

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Looks good, was just wondering why you removed the { assert process.success }, statements from the nf-test. I would add it back in and then approve this :)

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@mahesh-panchal mahesh-panchal left a comment

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Few small things still, but otherwise fine by me
The options should also be -- format, but -t doesn't have one it seems.

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@mashehu , do you want the change to the get-shards action to be merged in?

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@famosab famosab left a comment

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LGTM 🚀

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sofstam commented Jan 29, 2025

@SPPearce I will wait with merging then.

@sofstam sofstam added this pull request to the merge queue Jan 30, 2025
Merged via the queue into nf-core:master with commit cfe3660 Jan 30, 2025
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@sofstam sofstam deleted the sylph_profile branch January 30, 2025 10:00
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5 participants