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[Subworkflow][WIP] Tractoflow #177

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[Subworkflow][WIP] Tractoflow #177

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AlexVCaron
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Describe your changes

Subworkflow for Tractoflow here ! In addition there is also some changes to modules and subworkflows it depends on :

  • Implemented multiprocessing using nf-core pipeline labels
  • Replaced if/else by clever uses of .join() with remainder: true
  • Accelerate tests using the new 20 axial slices subject (newly created for Tractoflow, but we should use it everywhere)

The subworkflow does not include reading inputs from bids or other sources. For this, I'd rather we have another subworkflow doing the job.

The PR is quite big and could be chunked to single out individual module or subworkflow updates. We'll also see after the PR opens if the test infra responds well.

List test packages used by your module

Everything used by modules in nf-scil

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
    • 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 changed the title [SUBWORKFLOWS] Tractoflow [Subworkflow][WIP] Tractoflow Aug 6, 2024
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