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[Subworkflow] BundleSeg subworkflow. #146

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merged 13 commits into from May 14, 2024
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gagnonanthony
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@gagnonanthony gagnonanthony commented May 10, 2024

Describe your changes

Add BundleSeg as a subworkflow to be chained with nf-tractoflow. It might not be the most efficient way, but I made the Atlas directory optional. If provided, it must abide by the structure convention specified in the meta.yml. If not provided, the subworkflow will fetch the atlas and config archives directly from Zenodo.

@AlexVCaron and @arnaudbore, I'm open to suggestions!

List test packages used by your module

  • tracking.zip

Checklist before requesting a review

  • Create the tool:
    • Edit ./modules/nf-scil/<category>/<tool>/main.nf
    • Edit ./modules/nf-scil/<category>/<tool>/meta.yml
  • Generate the tests:
    • Edit ./tests/modules/nf-scil/<category>/<tool>/main.nf
    • Edit ./tests/modules/nf-scil/<category>/<tool>/nextflow.config
    • Add test data locally for tests with the fork repository
    • Generate the test infrastructure and md5sum for all outputs
  • Ensure the syntax is correct :
    • Check indentation abides with the rest of the library (don't hesitate to correct others !)
    • Lint everything. Ensure your variables have good names.

@gagnonanthony gagnonanthony added the assembly New module or subworflow for nf-scil label May 10, 2024
@gagnonanthony gagnonanthony self-assigned this May 10, 2024
@gagnonanthony gagnonanthony changed the title [Subworkflows] RecoBundlesX/BundleSeg subworkflow. [Subworkflow] RecoBundlesX/BundleSeg subworkflow. May 10, 2024
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@AlexVCaron AlexVCaron left a comment

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All good on my end, I'll let @arnaudbore comment on functionality. Great work, you're a rockstar 🚀

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@arnaudbore arnaudbore left a comment

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LGTM need a quick fix then 🎉

subworkflows/nf-scil/rbx/main.nf Outdated Show resolved Hide resolved
subworkflows/nf-scil/rbx/main.nf Outdated Show resolved Hide resolved
@gagnonanthony gagnonanthony changed the title [Subworkflow] RecoBundlesX/BundleSeg subworkflow. [Subworkflow] BundleSeg subworkflow. May 13, 2024
@arnaudbore arnaudbore merged commit c6a7340 into scilus:main May 14, 2024
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@gagnonanthony gagnonanthony deleted the rbx branch May 21, 2024 13:31
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3 participants