v1.4.0

What's Changed

• Added a pseudogene and spurious ORF detection workflow by @tgurbich in #49 and by @mberacochea in #51.
  Pseudofinder is used to identify pseudogenes, in addition to the pseudogene detection workflow that is part of Bakta. CDS with AntiFam hits are now removed from the final GFF output.
• Added output modifications, generation of an additional GFF file and README instructions to simplify ENA/GenBank submission by @tgurbich in #52.
• Mettannotator now uses the 'rRNA' feature for ribosomal RNA instead of grouping it with ncRNA as was done in previous versions. ncRNA classes are now added to the ninth column for ncRNA by @tgurbich in #52.
• Added tRNA locus tags by @tgurbich in #50
• Fixed temporary directory handling for multiple tools (Prokka, InterProScan, tRNAscan-SE, CRISPRCasFinder, AMRFinderPlus) by implementing process-specific tmp directories in workdir by @mberacochea in #46
• Added more instructions for Nextflow run by @mberacochea in #48

Full Changelog: v1.3...v1.4.0

v1.3

What's Changed

• Added citation by @tgurbich in #37
• Unifre mount issue with docker. by @mberacochea in #39 and #41
• Fixes for ref dbs mounts for docker in ips and unifire. Mem limit to emapper --dbmem flag by @mberacochea in #42
• Version bump to v1.3 for release by @mberacochea in #43

Full Changelog: v1.2...v1.3

v1.2

What's Changed

• Introduced the fast mode (--fast option) that allows to run mettannotator without InterProScan, UniFIRE and SanntiS, significantly reducing runtime and resource use.
• Sped up execution in regular mode by improving eggNOG-mapper runtime.
• Cleaned up function description in the product field of the final GFF file.
• Cleaned up product description for ncRNA.
• Bug fixes in the database download subworkflow.
• Bug fixes in function assignment.

Full Changelog: v1.1...v1.2

v1.1

What's Changed

• Added a --bakta flag to use Bakta instead of Prokka as the gene caller for bacterial genomes
• Enabled annotation of Archaea
• Added Circos plot generation
• Added a pre-processing script to help with the input file generation
• Updated AMRFinderPlus
• Added instructions for mobilome annotation
• UniFIRE bug fixes

Full Changelog: v1.0...v1.1

v1.0

Merge pull request #24 from EBI-Metagenomics/dev

Dev