feat: updated Nextflow workflows with profiles, auto-assess, rehoming

[FIrgolitsch]

PR #102 — Nextflow Workflow Updates

Rewrites the 3D reconstruction workflow to consume the new features from PRs #87, #97, #98, #100, #101, and adds a dedicated diagnostics workflow. Two commits: initial drop and a refactor of the reconstruction pipeline (~1100 lines rewritten) plus the new diagnostics.nf.

Changes

• workflows/reconst_3d/soct_3d_reconst.nf — major refactor. New processes:
  • auto-exclude based on slice-quality assessment (PR feat: diagnostic and analysis scripts #100) and motor-drift limits (PR feat: motor stacking, auto-exclude, refined stitching #98)
  • motor-only stacking + refined stitching path (PR feat: motor stacking, auto-exclude, refined stitching #98)
  • rehoming detection + reset using linum_detect_rehoming.py (PR feat: utility modules, preprocessing improvements, galvo correction #97)
  • MSE-based slice-quality gate before stitching
  • optional slice interpolation per slice_config.csv via linum_interpolate_missing_slice.py (PR feat: slice interpolation for missing sections (z-morph) #87), including the --finalise aggregation step
  • end-of-run HTML report via linum_generate_pipeline_report.py (PR feat: diagnostic and analysis scripts #100)
• workflows/reconst_3d/nextflow.config — new execution profiles (cpu, gpu, server, local), expanded params for every new feature, sensible defaults per profile
• workflows/reconst_3d/diagnostics.nf (new) — dedicated diagnostics-only workflow: runs linum_diagnose_pipeline, linum_analyze_shifts, linum_analyze_registration_transforms, linum_analyze_stitch_affine, linum_analyze_tile_dilation, linum_aggregate_dilation_analysis, then emits an HTML report. Can be run standalone against an existing reconstruction.
• workflows/preproc/preproc_rawtiles.nf — process tweaks to consume the updated galvo-shift / normalization scripts from PR feat: utility modules, preprocessing improvements, galvo correction #97
• workflows/preproc/nextflow.config — parameter and profile updates

Commits

1. feat: updated Nextflow workflows with profiles, auto-assess, rehoming
2. feat(workflow): refactor reconstruction pipeline, add diagnostics

Dependencies

• Stacked on PR feat: motor stacking, auto-exclude, refined stitching #98 (motor stacking) → PR feat: utility modules, preprocessing improvements, galvo correction #97 (utility/preprocessing) → PR build: migrate to uv, add ruff/ty, format all files #95 (build tooling)
• References scripts added by PRs feat: slice interpolation for missing sections (z-morph) #87, feat: utility modules, preprocessing improvements, galvo correction #97, feat: motor stacking, auto-exclude, refined stitching #98, feat: diagnostic and analysis scripts #100, feat: Allen atlas improvements and RAS alignment #101 — recommended merge order is bottom-up so each process's referenced script already exists on main