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Published April 20, 2020 | Version v1.3.1
Software Open

bactopia/bactopia: QOL improvements and bug fixes

Authors/Creators

  • 1. Emory University

Description

v1.3.1 bactopia/bactopia "Emperor Hairpin" - 2020/04/20 Added
  • summary tool now gives reason for rank
  • summary tools now splits failed into exclude and qc-failure
  • Better documentation on how --cpus works in Nextflow
  • Efficiency info when executed on standard profile
  • split blast_query into blast_genes, blast_primers and blast_proteins
  • mapping_query now creates multifasta of fastas at maps at once then splits per-base coverage into separate files
  • --nfconfig users can provide their own Nextflow config file
  • fastani users can provide their own reference now
  • bactopia versions will print versions for tools used by Bactopia
  • bactopia citations will print citations for tools and datasets used by Bactopia
  • bactopia search can filter based on total bases, mean read length, and missing FASTQs
  • blast queries results are only JSON format for easy parsing later
  • added --compliant option for Prokka annotation
Fixed
  • build-containers.sh not working with Bactopia Tools
  • Bactopia Tools container tools missing environment.yml
  • Typo in fastani usage
  • Samples with multiple QC errors counted for each error
  • Incorrect ISMapper version
  • typo in summary SLURM profile
  • gtdb Singularity container not mounting path to GTDB database
  • roary missing rename in containers
  • blast_query results overwriting one another
  • build-containers.sh now creates a "latest" tag
  • bactopia tool roary outputs results based on the given prefix
  • renamed --addgenes to --nogenes
  • updated ASA³P citation
  • Typos in Bactopia Tools docs
  • Link in README.md

Files

bactopia/bactopia-v1.3.1.zip

Files (20.3 MB)

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Additional details

Related works

Is supplement to
https://github.com/bactopia/bactopia/tree/v1.3.1 (URL)