v3.2.0 bactopia/bactopia "Black Bulls" 2025/03/21

"Black Bulls" is related to the best magic squad in Black Clover my kids currently watching

Added

• Bactopia Tools (bactopia --wf <NAME>)
  • checkm2 - Rapid assessment of genome bin quality using machine learning @maxlcummins
  • sylph - taxonomic profiling and genome querying for meta-genomic samples
• teton now outputs a bactopia sample sheet with species and genome size filled out
  • sizemeup uses the bracken output to determine genome size
• more metrics and helper text at end of runs
• snippy use a local directory for --tmpdir
• bactopia atb-downloader to download ATB assemblies by BioSample, TaxID, or species
• pangenome add SNP dists for both masked and unmasked alignments
• within task clean up to help reduce work directory size
  • gtdb: add --gtdb_keep_msa to keep GTDB MSA files, otherwise remove
  • kraken2: replace --remove_filtered_reads with --keep_filtered_reads to keep classified and unclassified reads
  • ncbigenomedownload: add --keep_genomes to publish downloaded genomes, default leave in work directory
    • this also affects Prokka annotations in the pangenome workflow
  • snippy: add --snippy_remove_bam to remove BAM files after variant calling
• support for custom databases in emmtyper @maxlcummins
• bump program versions in modules
  • amrfinderplus: 3.12.8 -> 4.0.19
  • bactopia-teton: 1.0.2 -> 1.1.1
  • bakta: 1.9.4 -> 1.11.0
  • busco: 5.7.1 -> 5.8.2
  • csvtk: 0.27.2 -> 0.31.0
  • gubbins: 3.3.5 -> 3.4
  • iqtree: 2.2.2.7 -> 2.3.6
  • kleborate: 3.0.9 -> 3.1.3
  • multiqc: 1.24.1 -> 1.27.1
  • panaroo: 1.5.0 -> 1.5.1
  • quast: 5.2.0 -> 5.3.0
  • sister: 1.1.2 -> 1.1.3
  • sylph: 0.6.1 -> 0.8.0
  • tbprofiler: 6.3.0 -> 6.6.2

Fixed

• debugging print in functions.nf
• fixed params.max_retry in local profiles
• nextflow.config accessing param vals before they are set
• removed lingering task.ext which were not used
• replace --singularity_cache_dir with --singularity_cache to match bactopia download
• gamma not checking for --gamma_db at runtime
• tests using single protein (typo in file name config)
• pangenome mislabeling pangenome tool used (was using the correct tool)
• downloaded genomes added to --bactopia directory for pangenome
• useless use of options.btype ?: in modules (it didn't actually do anything because options.btype was always empty)
• version capture in dragonflye and mlst
• mismatch in defensefinder conda and container versions
• kraken-bracken-summary.py failing with 0 unclassified reads @maxlcummins