v0.1.0 - [2024-03-22]

Initial release of phac-nml/mikrokondo. Mikrokondo currently supports: read trimming and quality control, contamination detection, assembly (isolate, metagenomic or hybrid), annotation, AMR detection and subtyping of genomic sequencing data targeting bacterial or metagenomic data.

What's Changed

• updated docs by @mattheww95 in #1
• updated citations by @mattheww95 in #2
• updated docs by @mattheww95 in #3
• Dev by @mattheww95 in #4
• reintegrated shigeifinder by @mattheww95 in #5
• added workflow stubs by @mattheww95 in #6
• Dev by @mattheww95 in #7
• Dev by @mattheww95 in #8
• Dev by @mattheww95 in #10
• Nf validate by @mattheww95 in #11
• Dev by @mattheww95 in #12
• Updated Configuration settings and fixed minor reporting issues by @mattheww95 in #18
• updated docs by @ChristyPeterson in #26
• Adding nf-test tests by @apetkau in #27
• Dev by @mattheww95 in #28
• Disabled tracing by default for testing by @apetkau in #29
• Dev by @mattheww95 in #30
• sync dev with main by @mattheww95 in #32
• Add tests for qc_assemblies subworkflow by @apetkau in #31
• Dev by @emarinier in #33
• Dev by @mattheww95 in #35
• Adding Integration Testing by @emarinier in #34
• Add/linting by @apetkau in #37
• Iridanext plugin by @mattheww95 in #36
• Ignores pre-commit check on README for now by @apetkau in #40
• Adding Additional Testing by @emarinier in #42
• Tests/from assemblies by @apetkau in #41
• Updates schema_input.json for integration with IRIDA Next by @apetkau in #45
• Fix json flattening by @mattheww95 in #47
• Tests/from assemblies other by @apetkau in #46
• nested nextflow schema params by @mattheww95 in #49
• Fix/cleanup iridanext outputs by @apetkau in #50
• Fix/customdumpsoftwareversions by @apetkau in #51
• Docs update by @ChristyPeterson in #38
• bumped version by @mattheww95 in #52
• Dev by @mattheww95 in #54

New Contributors

• @mattheww95 made their first contribution in #1
• @ChristyPeterson made their first contribution in #26
• @apetkau made their first contribution in #27
• @emarinier made their first contribution in #33

Full Changelog: https://github.com/phac-nml/mikrokondo/commits/0.1.0