bge-barcoding/BeeGees: v3.0.6

Zenodo (CERN European Organization for Nuclear Research)

Abstract

The bioconda recipe was missing bbmap (reformat.sh, used by the optional downsampling rules), samtools, wget (download_taxdump) and r-yaml (library(yaml) in multiqc_plots.R, previously satisfied only as a transitive tidyverse dependency). Enabling downsampling.enabled or setting fasta_cleaner.reference_dir on a conda install failed with a missing binary. Removed the undeclared bc dependency from the MitoGeneExtractor rules, which used it only to format a file size for the log. Replaced with numfmt, already used throughout the Snakefile. bc was on the default execution path and present in no environment file. 04_reference_filter.py no longer exits when samtools is absent. samtools supplies only the flagstat summary; filtering itself parses SAM flags in pure Python. A missing samtools now warns and reports zeroed statistics. Removed beegees_env.yaml and rewrote the installation docs around conda install -c conda-forge -c bioconda beegees. run_local.sh and run_slurm.sh now pass --config config/config.yaml, matching the layout beegees init creates rather than a clone-relative path.

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