bge-barcoding/BeeGees: v3.0.4

Zenodo (CERN European Organization for Nuclear Research)

Abstract

Bug fixes Fix SpawnedJobError in create_alignment_log rules - Snakemake 8 auto-classifies low-resource run: blocks as local and spawns them as subprocesses, where lambda-resolved input file lists are not reliably serialised. Affected rules (create_alignment_log_concat, _merge, _se) are rewritten to use shell: find instead, resolving silent failures when running --profile local. Fix --log-file writing only at end of run - the log file is now written line-by-line (flushed after each line) rather than in OS-buffered bursts, so --log-file beegees.log behaves like a live tee for the full run. Fix double-write in run_slurm.sh - removed | tee beegees.log from the SLURM helper script, which was opening the same file as --log-file simultaneously. Changes version now reads from package metadata - beegees/init.py derives version from the installed package (via importlib.metadata), so only pyproject.toml needs updating on each release. Updated rule resource allocations in config.yaml — corrected thread counts for single-threaded tools (MitoGeneExtractor, structural validation) and reduced memory limits where over-allocated. Docs - expanded README with correct output paths, CLI usage, and MultiQC section; moved README_hmm_info.md to docs/.

Authors 4

1. Dan Parsons
2. Claude

   Anthropic (United States)

   Affiliation as printed

   @anthropics

3. Rutger Vos Aachen Naturalis Biodiversity Center

   Naturalis Biodiversity Center

   Affiliation as printed

   Naturalis Biodiversity Center

4. Ben Price
   Affiliation as printed

   @NaturalHistoryMuseum