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[New module] Module Synthseg #6

Merged
merged 10 commits into from
Sep 26, 2024
Merged

[New module] Module Synthseg #6

merged 10 commits into from
Sep 26, 2024

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anroy1
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@anroy1 anroy1 commented Sep 24, 2024

Filling your PR description

add synthseg segmentation module from freesurfer 7.4.

List test packages used by your module

  • heavy.zip

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  • 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.

AlexVCaron
AlexVCaron requested changes Sep 24, 2024
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Another great PR ! Not much to say, everything is syntax and wording. It,s going on well, once done LGTM !

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@AlexVCaron AlexVCaron requested review from GuillaumeTh and removed request for gagnonanthony September 24, 2024 18:22
AlexVCaron
AlexVCaron requested changes Sep 26, 2024
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Two little things to fix. Also, add the segmentation in the module's outputs and test it's md5SUM as well. We'll know then if mri_synthseg is the source of the problem.

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@AlexVCaron AlexVCaron added this pull request to the merge queue Sep 26, 2024
Merged via the queue into scilus:main with commit 3a9a336 Sep 26, 2024
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@anroy1 anroy1 deleted the synthseg2 branch September 27, 2024 14:26
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@AlexVCaron AlexVCaron AlexVCaron approved these changes

@GuillaumeTh GuillaumeTh Awaiting requested review from GuillaumeTh

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@anroy1 @AlexVCaron