Add segger transcript assignment (CLI-based)#168
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Rework the segger draft to run segger's end-to-end CLI (`segger segment`) instead of the Python API that was stuck on segger issue #126. - script.py: derive boundary prior from the provided segmentation, write a Xenium-layout dir (transcripts + cell/nucleus boundaries parquet), invoke `segger segment`, then map the per-transcript assignments back onto the transcripts and write the standard transcript_assignments output. Includes the multi-partition parquet transcript-transform index fix. - config.vsh.yaml: switch engine to nvcr.io/nvidia/pytorch base + dpeerlab/segger (the maintained fork with the CLI); expose n_epochs, prediction_expansion_ratio, prediction_mode arguments; gpu nextflow label. - run_test_segger_nebius.sh: Nebius test run on test resources, default method at every stage plus segger in the transcript-assignment stage. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Rework the segger draft to run segger's end-to-end CLI (
segger segment) instead of the Python API that was stuck on segger issue #126.segger segment, then map the per-transcript assignments back onto the transcripts and write the standard transcript_assignments output. Includes the multi-partition parquet transcript-transform index fix.Describe your changes
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Proposed changes are described in the CHANGELOG.md
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