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