[0.5.0] - 2024-11-27

[0.5.0] - 2024-11-27

Added

• Added RASUSA for down sampling of Nanopore or PacBio data. PR 125

• Added a new sample_name field to the schema_input.json file: PR 140

• Incorporated a --skip_read_merging parameter to prevent read merging PR 140

Changed

• Added a sample_name field, sample still exists but is used to incorporate additional names/identifiers in IRIDANext PR 140

• RASUSA now used for down sampling of Nanopore or PacBio data. PR 125

• Default Listeria quality control parameters apply only to monocytogenes now. PR 142

Updated

• Documentation and workflow diagram has been updated. PR 123

• Documentation and Readme has been updated. PR 126

• Adjusted schema_input.json to allow for non-gzipped inputs. PR 137

• Updated github actions workflows for nf-core version 3.0.1. PR 137

Thank you to: @apetkau, @sgsutcliffe and @kylacochrane for all your contributions!

[0.4.2] - 2024-09-25

[0.4.2] - 2024-09-25

Fixed

• Fixed broken link in readme. PR 117

• Fixed ectyper parameter types in the nextflow_schema.json from number to integer. PR 121

Thank you @apetkau for testing things in the cloud ☁️

[0.4.1] - 2024-09-16

[0.4.1] - 2024-09-16

Fixed

• Fixed null species ID in QCMessage when no organism qc data available. PR 111

Changed

• Removed missing alleles from final report fixing issue 112.

• Changed default option for override_allele_scheme from null to "" (evaluates to false). PR 109

[0.4.0] - 2024-09-04 Back to School

[0.4.0] - 2024-09-04

Changed

• Removed quay.io docker repo tags PR 94

Updated

• Added QCMessage and QCSummary fields for metagenomic sequencing runs. See PR 103

• Updated TSeemann's MLST default container to use version 2.23.0 of mlst. See PR 97

• Moved allele schema parameters under one option in the nextflow_schema.json. See PR 104

Fixed

• Fixed typo in metagenomic QC message. See PR 103

• Fixed spelling issues issues in config values. See PR 95

• Fixed the headers specified in the nextflow.config file for Kraken2. See PR 96

Added

• Added additional organism QC parameters to defaults. See PR 105

• Updated locidex to version 0.2.3. See PR 96

• Added module for automatic selection of locidex databases through configuration of a locidex database collection. See PR 96

• Added module for summary of basic allele metrics, listing of missing alleles and reporting of specific alleles. See PR 96

A lot of changes were made in this release thanks to the help of many people:

• @apetkau for his feedback, code reviews and ability to trouble shoot bugs and errors 🐛 🦅
• @kylacochrane for code reviews, feedback and improvements of the locidex_select.nf module. The code is now a lot more groovy💃⚡
• @emarinier for code reviews, discussions, feedback and suggestions on the locidex_select.nf module. 🤖 🍻
• @sgsutcliffe for integrating support of alternative container registries 🚀 🧪

[0.3.0] - 2024-07-04

[0.3.0] - 2024-07-04

Changed

• Reformatted QCSummary fields and added a QCMessage field containing the old summary message. See PR 85

• Changed default Python3 image to use the StarAMR image. See PR 90

• Stripped identifier from taxonomic identification from string. See PR 90

• Removed retry logic from processes and switched them to ignore. See PR 91

Fixed

• Updated samtools/minimap2 container fixing CI issues and issues running the pipeline with Docker. See PR 85

• Removed task.maxRetries from error handling to prevent StackOverflow addressing PR 91

Added

• Altered name of stored SpeciesTopHit field in the irida-next.config, and added a field displaying the field name used addressing PR 90

Thank you so much @apetkau for all of your support!

[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