ci(nextflow): nf-test infrastructure and GitHub Actions workflow

[FIrgolitsch]

Stacked PR 10/22 — review order: #115 → #97 → #98 → #99 → #100 → #101 → #108 → #106 → #107 → #87 → #116 → #110 → #111 → #40 → #112 → #113 → #117 → #118 → #120 → #121 → #122 → #123 → #124 → #125

Base: pr-n4-bias-field. Retargets to main as upstream PRs merge.

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PR #110 — Nextflow CI: nf-test infrastructure + workflow streamline

Adds end-to-end testing for Nextflow pipelines using nf-test (all processes invoked in stub mode so tests run without real imaging data) and streamlines the workflow files to share configuration between pipelines.

Streamline refactor (one commit)

refactor(workflows): streamline configs, extract cpu_limits.config and Helpers.groovy

• New workflows/shared/cpu_limits.config — single source of truth for enable_cpu_limits / max_cpus / reserved_cpus / processes and the beforeScript thread-cap closure, included by both pipelines
• New workflows/reconst_3d/lib/Helpers.groovy — moves all the helper functions out of soct_3d_reconst.nf (303 lines extracted), auto-loaded by Nextflow via the lib/ convention
• Consolidates publishDir calls and standardises on ${params.X} interpolation
• Reorders sections in nextflow.config so the file reads top-down: params → process config → profiles
• Net change: 6 files, +120/−386

CI (one squashed commit)

ci(nextflow): make CI green — pin nf-test 0.9.5, fix .gitignore for lib/ and zarr stubs, filter lint false-positives, cap test processes

• .github/workflows/nextflow-ci.yml: triggers on workflows/** and .github/workflows/nextflow-ci.yml changes (main, dev); pinned to nf-test 0.9.5 (latest broke compilation by not auto-loading lib/); ANSI-strip + awk filter on lint output to drop the 29 known Helpers.X(...) false-positives that nextflow lint reports because it doesn't load Groovy classes from lib/
• .gitignore: re-include rules for workflows/**/lib/** (was caught by the Python lib/ ignore — Helpers.groovy was never pushed) and for *.ome.zarr directories under tests/data/ (was caught by the *.zarr ignore — stub .gitkeep placeholders were never pushed)
• nf-test.config: root nf-test configuration; tests/nextflow.config: shared test config
• Stub blocks added to all processes in preproc_rawtiles.nf and soct_3d_reconst.nf

Tests

• workflows/preproc/tests/preproc_rawtiles.nf.test — stub-run preproc pipeline (minimal tile inputs in workflows/preproc/tests/data/session_01/...)
• workflows/reconst_3d/tests/soct_3d_reconst.nf.test — stub-run reconst pipeline (minimal shifts_xy.csv and mosaic_grid_z*.ome.zarr placeholders); processes = 2 cap on the optional-branch test so it fits 4-CPU GitHub-hosted runners