v2.2.1

• Hot fix for missing/incorrect Singularity image configurations

v2.2.0

• Pipeline now accepts genome assemblies as inputs. Samplesheet format: id,/path/to/fasta (Currently cannot build QC report from assembly inputs; Annotation report works)
• Fixed missing medaka container in Singularity profile
• Improved support for medaka model specification through automated model download from here

v2.1.0

• Changes to meta option to allow users to selectively analyze their species of interest in metagenomic data (off/targeted/untargeted)
• Ability to control the maximum resource limits for all Nextflow processes using max_cpus, max_time, max_memory
• Added medaka_model option to specify Medaka models for genome polishing
• Updated medaka version to 1.11.3 to support the latest chemistries
• Fixed OOM error when summarizing rgi results

v2.0.0

• Ability to execute the workflow in real-time
• Additional read quality filtering options --min_rl, --min_rq, --min_tr
• Option to disable genome polishing with --nopolish
• QC report now reports target DNA output in total read count and bases
• Updated EPI2ME compatibility (v5.1.10)

v1.6.15

• Optimized the publishing of genome assembly outputs

v1.6.14

• Replaced seqkit docker image with the biocontainer image

v1.6.13

• Update process resource usage optimized by Nextflow Tower
• Fixed --nano-hq parameter for Flye assembler
• Updated metaFlye assembly parameter for metagenome assembly

v1.6.12

• Updated CCTyper to v1.8.0
• Use Flye v2.9.2 for MAG assembly (--meta option)

v1.6.11

• Failed samples are ignored in Annotation HTML reports
• The pipeline now publishes Dragonflye assemblies in .gfa and .fasta format

v1.6.10

• Allow for duplicated gene feature names across genome annotation types (AMR/VF/Plasmids)
• Fixed error when --qc is not invoked
• Genome assembly error handling is now set to ignore. Downstream processes are skipped for failed genome assemblies.