[0.9.1] - 2025-08-15

`Fixed`

Fixed issue with incorrect cardinality of elements passed to channel in hybrid assemblies. PR 184

- Nextflow
Published by mattheww95 7 months ago

0.9.0 - 2025-08-11

`Changed`

Changed default search parameter for Escherichia coli to Escherichia. PR 181
Removed individual seven gene mlst results from IRIDANext config. PR 180
fastq_scan.py script was refactored to reduce resource usage. PR 179

`Fixed`

Added missing report_tag value to rasusa in the nextflow.config file which was causing Issue #182. PR 181

- Nextflow
Published by mattheww95 7 months ago

0.8.1 - 2025-07-04

`Added`

When --skip_version_gathering is false, a {sample}.mikrokondo.parameters.json and {sample}.mikrokondo.software.version.yml is generated. These files collect all the software versions used in the pipeline and the parameters selected. Note: Parameters are recorded at the pipeline level, individual sample parameters are not included.

- Nextflow
Published by sgsutcliffe 8 months ago

[0.8.0] - 2025-06-19

`Changed`

Added predicted_primary_type_name, predicted_primary_type_method, predicted_secondary_type_name, and predicted_secondary_type_method fields, which are output to Irida Next as PrimaryTypeID, PrimaryTypeIDMethod, SecondaryTypeID, and SecondaryTypeIDMethod, respectively. PR 168

- Nextflow
Published by emarinier 8 months ago

0.7.1 - 2025-05-22

`Changed`

Fixed container string for ectyper docker and singularity containers. PR 173

- Nextflow
Published by apetkau 9 months ago

0.7.0 - 2025-05-21

`Changed`

Renamed n50 Status and n50 Value to qc_status_assembly_n50 and n50_value respectively. PR 166
Added the ECTyper speciation results to shigella outputs. PR 166

`Update`

Update SISTR docker/singularity build (1->2). PR 170
Update ECTyper docker/singularity build (3->4). PR 170

- Nextflow
Published by apetkau 9 months ago

mikrokondo - [0.6.1] - 2025-04-28

`Fixed`

Updated new parameter positions in nextflow_schema.json

- Nextflow
Published by mattheww95 10 months ago

mikrokondo - [0.6.0] - 2025-04-25

[0.6.0] - 2025-04-25

`Changed`

Updated StarAMR to latest release v0.11.0 and modified tests to reflect new outputs. PR 153
Changed the name of multiple metadata fields mentioned in issue 148. PR 159.
Updated ECTyper to version 2.0.0 and SISTR to version 1.1.3 PR 161.
Shigella samples are now fed into ECTyper version 2.0.0 PR 161.

`Added`

Added mikrokondo version to the output reports. PR 160
Added new control flow parameter fail_on_metagenomic which prevents samples from undergoing additional downstream processing. PR 158
Added additional logic for setting the predicted_id and predicted_id_method fields. PR 159

- Nextflow
Published by mattheww95 10 months ago

mikrokondo - [0.5.1] - 2025-02-25

[0.5.1] - 2025-02-25

`Added`

Added a configuration file conf/equivalent_taxa.json for denoting equivalent taxa to prevent falsely flagging samples as metagenomic when multiple genera are present. PR 150

- Nextflow
Published by mattheww95 about 1 year ago

mikrokondo - [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!

- Nextflow
Published by mattheww95 over 1 year ago

mikrokondo - [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 ☁️

- Nextflow
Published by mattheww95 over 1 year ago

mikrokondo - [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

- Nextflow
Published by mattheww95 over 1 year ago

mikrokondo - [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 🚀 🧪

- Nextflow
Published by mattheww95 over 1 year ago

mikrokondo - [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!

- Nextflow
Published by mattheww95 over 1 year ago

mikrokondo - [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!

- Nextflow
Published by mattheww95 over 1 year ago

mikrokondo - 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

- Nextflow
Published by mattheww95 almost 2 years ago

mikrokondo - v0.1.2 - [2024-05-02]

Changed

Changed default values for database parameters --dehostingidx, --mashsketch, --kraken2db, and --baktadb 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.

- Nextflow
Published by mattheww95 almost 2 years ago

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.

- Nextflow
Published by apetkau almost 2 years ago

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

New Contributors

@mattheww95 made their first contribution in https://github.com/phac-nml/mikrokondo/pull/1
@ChristyPeterson made their first contribution in https://github.com/phac-nml/mikrokondo/pull/26
@apetkau made their first contribution in https://github.com/phac-nml/mikrokondo/pull/27
@emarinier made their first contribution in https://github.com/phac-nml/mikrokondo/pull/33

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

- Nextflow
Published by mattheww95 almost 2 years ago

Recent Releases of mikrokondo

mikrokondo - 0.9.1

[0.9.1] - 2025-08-15

Fixed

mikrokondo - 0.9.0

0.9.0 - 2025-08-11

Changed

Fixed

mikrokondo - 0.8.1

0.8.1 - 2025-07-04

Added

mikrokondo - 0.8.0

[0.8.0] - 2025-06-19

Changed

mikrokondo - 0.7.1

0.7.1 - 2025-05-22

Changed

mikrokondo - 0.7.0

0.7.0 - 2025-05-21

Changed

Update

mikrokondo - [0.6.1] - 2025-04-28

Fixed

mikrokondo - [0.6.0] - 2025-04-25

[0.6.0] - 2025-04-25

Changed

Added

mikrokondo - [0.5.1] - 2025-02-25

[0.5.1] - 2025-02-25

Added

mikrokondo - [0.5.0] - 2024-11-27

[0.5.0] - 2024-11-27

Added

Changed

Updated

mikrokondo - [0.4.2] - 2024-09-25

[0.4.2] - 2024-09-25

Fixed

mikrokondo - [0.4.1] - 2024-09-16

[0.4.1] - 2024-09-16

Fixed

Changed

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

[0.4.0] - 2024-09-04

Changed

Updated

Fixed

Added

mikrokondo - [0.3.0] - 2024-07-04

[0.3.0] - 2024-07-04

Changed

Fixed

Added

mikrokondo - [0.2.1] - 2024-06-04

[0.2.1] - 2024-06-04

Fixed

mikrokondo - v0.2.0 - [2024-05-14]

v0.2.0 - [2024-05-14]

Added

Fixed

Changed

mikrokondo - v0.1.2 - [2024-05-02]

Changed

mikrokondo - Version 0.1.1

v0.1.1 - [2024-04-22]

Added

Changed

mikrokondo - v0.1.0 - [2024-03-22]

What's Changed

New Contributors

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