feat: updated Nextflow workflows with profiles, auto-assess, rehoming#108
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Two fixes that together stop temp zarrs from filling /tmp: 1. Default dir from None (=> tempfile.gettempdir() => /tmp) to '.' (CWD, typically the Nextflow task work dir). Even if the temp dir leaks, it's reclaimed when the work dir is cleaned, and never lands on small /tmp partitions. 2. Replace TemporaryDirectory(...).name (which discards the cleanup handle the moment .name is read; cleanup then depends on a fragile weakref finalizer that doesn't run on SIGKILL) with mkdtemp() plus atexit.register(shutil.rmtree, ..., ignore_errors=True). atexit fires on normal interpreter shutdown regardless of which file handles zarr still holds open. Symptom: 14 stale tmp*.zarr dirs (~5 GB) in /tmp on the lab server, contributing to ENOSPC on /tmp during reconstruction.
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PR #108 — Updated Nextflow Workflows (profiles, auto-assess, rehoming)
Replaces the accidentally-merged-then-reverted #102. Modernises the Nextflow workflows to consume the new library and script outputs from #97–#101.
Workflow changes
local,beluga,dockerexecutionlinum_assess_slice_quality.py)linum_detect_rehoming.py)linum_stitch_3d_refined.py)linum_align_to_ras.py)Nextflow v26 strict-DSL compatibility
The follow-up commit
fix(workflows): make Nextflow v26 strict-DSL compatibleensures the workflow runs cleanly under Nextflow ≥ 26.04 (still compatible with the declared>= 23.10minimum):getAvailableCpus()into thebeforeScriptclosure (top-leveldefno longer allowed in v26 config DSL)(int)(...)casts withas int(v26 parses the C-style form as a method call)publishDirpaths that reference$task.*in closures (lazy eval is now required)nextflow lintclean on bothreconst_3dandpreprocpipelines under Nextflow 26.04.0Streamline + extract refactor (lives downstream on #110)
The configs are further streamlined on #110 (
refactor(workflows): streamline configs, extract cpu_limits.config and Helpers.groovy) — kept there because it depends on thecorrect_bias_fieldprocess introduced by #109. Reviewers reviewing the Nextflow stack should look at #108 first, then #109, then #110.