[0.2.1] - 2024-06-04

[0.2.1] - 2024-06-04

Fixed

• Parsed table values would not show up properly if values were missing resolving issue See PR 83
• Fixed mismatched description for minimap2 and mash databases. See PR 83

Thank you so much @apetkau for all the work you did to get this patch to work!

v0.2.0 - [2024-05-14]

v0.2.0 - [2024-05-14]

Added

• Updated documentation for params. See PR 66

• Fixed param typos in schema, config and docs. See PR 66

• Added parameter to skip length filtering of sequences. See PR 66

• Added locidex for allele calling. See PR 62

• Updated directory output structure and names. See PR 66

• Added tests for Kraken2 contig binning. See PR 66

Fixed

• If you select to filter contigs by length, those contigs will now be used for subsequent analysis. See PR 66

• Matched ECTyper and SISTR parameters to what is set in the current IRIDA. See PR 68

• Updated StarAMR point finder DB selection to resolve error when in db selection when a database is not selected addressing issue. See PR 74

• Fixed calculation of SeqtkBaseCount value include counts for both pairs of paird-end reads. See PR 65.

Changed

• Changed the specific files and metadata to store within IRIDA Next. See PR 65

• Added separate report fields for (PASSED|FAILED|WARNING) values and for the the actual value. See PR 65

• Updated StarAMR to version 0.10.0. See PR 74

v0.1.2 - [2024-05-02]

Changed

• Changed default values for database parameters --dehosting_idx, --mash_sketch, --kraken2_db, and --bakta_db to null.
• Enabled checking for existance of database files in JSON Schema to avoid issues with staging non-existent files in Azure.
• Set --kraken2_db to be a required parameter for the pipeline.
• Hide bakta parameters from IRIDA Next UI.

Version 0.1.1

v0.1.1 - [2024-04-22]

Added

Changed

• Switched the resource labels for parse_fastp, select_pointfinder, report, and parse_kat from process_low to process_single as they are all configured to run on the local Nextflow machine.

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