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Verify Remove contaminants reads come out in order.

Status: Open.

#221 In phac-nml/mikrokondo;

· mattheww95 opened on Apr 28, 2026

Optimization of stx Gene Sensitivity in IRIDANext/MK Pipeline as part of E.coli typimg via ECTyper

enhancementNew feature or requestNew feature or request

Status: Open.

#216 In phac-nml/mikrokondo;

· kbessonov1984 opened on Mar 6, 2026

Different values for CheckM when tests are run locally with Docker or Apptainer

invalidThis doesn't seem rightThis doesn't seem right

Status: Open.

#185 In phac-nml/mikrokondo;

· mattheww95 opened on Aug 15, 2025

Missing Kraken2 Speciation results in IRIDANext

Status: Open.

#167 In phac-nml/mikrokondo;

· mattheww95 opened on Apr 30, 2025

Kraken2 default confidence value

enhancementNew feature or requestNew feature or request

Status: Open.

#162 In phac-nml/mikrokondo;

· mattheww95 opened on Apr 22, 2025

Use Dorado instead of Medaka for polishing.

enhancementNew feature or requestNew feature or request

Status: Open.

#151 In phac-nml/mikrokondo;

· mattheww95 opened on Feb 14, 2025

Integrate Autocycler for hybrid assembly polishing

enhancementNew feature or requestNew feature or request

Status: Open.

#147 In phac-nml/mikrokondo;

· mattheww95 opened on Jan 3, 2025

Add mikrokondo-tools samplesheet to docs

enhancementNew feature or requestNew feature or request

Status: Open.

#138 In phac-nml/mikrokondo;

· mattheww95 opened on Oct 23, 2024

Upgrade to fastplong for nanopore workflow

enhancementNew feature or requestNew feature or request

Status: Open.

#136 In phac-nml/mikrokondo;

· mattheww95 opened on Oct 21, 2024

Incorporate database hashes or container has in output

enhancementNew feature or requestNew feature or request

Status: Open.

#135 In phac-nml/mikrokondo;

· mattheww95 opened on Oct 21, 2024

Add Btyper3 to workflow

enhancementNew feature or requestNew feature or request

Status: Open.

#134 In phac-nml/mikrokondo;

· mattheww95 opened on Oct 21, 2024

Upgrade to nf-schema from nf-validation

enhancementNew feature or requestNew feature or request

Status: Open.

#133 In phac-nml/mikrokondo;

· mattheww95 opened on Oct 21, 2024