0.9.4 - 2025-09-25 (Madam Bo)

0.9.4 - 2025-09-25

Added

• Added a IRIDA Next specific parameter: max_samples. max_samples is used to limit the number of samples the pipeline will run with. When the number of samples is >= max_samples all processes are skipped an an error file is produced max_samples_exceeded.error.txt. PR 191

[0.9.3] - 2025-09-12 (Shao Kahn)

[0.9.3] - 2025-09-12

Fixed

• Locidex failures in due to incorrect container logic in IRIDANext. PR 192

As mikrokondo is abbreviated to MK internally, @kbessonov1984 pointed out that it maybe worth figuring out a way to incomporate Mortal Kombat into the project somehow. Going forward releases will start having a Mortal Kombat reference attached to them.

Thanks again for the suggestion! @kbessonov1984

0.9.2 - 2025-09-12

Updated

• Updated locidex to version 0.4.0. PR 189

Changed

• Renamed metadata field TotalLoci to TotalLociInSchme. PR 189

• Renamed metadata field AllelesPresent to LociPresent. PR 189

• Locidex default report mode is now conservative mode instead of normal. PR 189

Added

• Metadata fields, locidex_loci_no_blast_hit, locidex_loci_single_blast_hit, locidex_loci_with_mulitple_values, locidex_loci_no_nucleotide_hits and locidex_loci_no_protein_hits. PR 189

0.9.1

[0.9.1] - 2025-08-15

Fixed

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

0.9.0

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

0.8.1

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.

0.8.0

[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

0.7.1

0.7.1 - 2025-05-22

Changed

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

0.7.0

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

[0.6.1] - 2025-04-28

Fixed

• Updated new parameter positions in nextflow_schema.json