bge-barcoding/BeeGees: v3.0.5

Zenodo (CERN European Organization for Nuclear Research)

Abstract

Taxonomic validation: tv_local_blast.py now batches queries into chunks of 50 sequences per blastn invocation instead of running one process per sequence, so a large reference database is loaded once per chunk rather than once per barcode. Per-sequence TSV outputs, the summary CSV layout and resume behaviour are unchanged. A failed chunk retries its sequences individually, and sequences that still fail now cause a non-zero exit (with no summary CSV) rather than being reported as no-match; --allow-partial-failures restores the previous leniency. Fixed the summary CSV dropping all hits for sequences whose FASTA header carries a description, where BLAST's qseqid (first token only) did not match the sanitized full header used as the CSV key. Removed the unused blast_options entry from the Snakefile's taxonomic_validation fallback, and corrected the documented BLAST hit limit (100, not 500). Structural validation: fixed a temp-file leak in structural_validation.py, where the per-sequence nhmmer query and tabular files were created with delete=False and never removed, leaving two files per sequence in TMPDIR (48 per sample, since each sample is validated across 6 parameter combinations and 4 input FASTAs). Structural validation: added --threads, passed from the rule, setting nhmmer's --cpu per invocation. Defaults to 1, so standalone behaviour is unchanged. Right-sized the rule resources to be flexible (to a degree) regardless of sample sizes run. Resource allocations, considering retry memory scaling should work with 1 or >500 samples.

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