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Removing params from any .nf file except for the root main.nf.

Status: Open.

#296 In nf-core/viralmetagenome;

· Joon-Klaps opened on Jun 2, 2026

Switch from deprecated Prokka to Pharokka

enhancementNew feature or requestNew feature or request

Status: Open.

#286 In nf-core/viralmetagenome;

· Joon-Klaps opened on Apr 11, 2026

·  

release 1.2.0

Krona and bracken not compatible

bugSomething isn't workingSomething isn't working

Status: Open.

#285 In nf-core/viralmetagenome;

· Joon-Klaps opened on Apr 11, 2026

Optionally remove unmapped reads from downstream alignment outputs

enhancementNew feature or requestNew feature or request

Status: Open.

#282 In nf-core/viralmetagenome;

· Joon-Klaps opened on Apr 1, 2026

Optionally use host-filtered reads in downstream mapping steps

enhancementNew feature or requestNew feature or request

Status: Open.

#281 In nf-core/viralmetagenome;

· Joon-Klaps opened on Apr 1, 2026

Suggestions for Improving nf-core/viralmetagenome Pipeline Efficiency and Robustness

enhancementNew feature or requestNew feature or request

Status: Open.

#280 In nf-core/viralmetagenome;

· NailouZhang opened on Apr 1, 2026

Allow Pre-built BLAST database

enhancementNew feature or requestNew feature or request

Status: Open.

#268 In nf-core/viralmetagenome;

· averagehat opened on Feb 25, 2026

·  

release 1.2.0

Explore capabilities of vclust

enhancementNew feature or requestNew feature or request

Status: Open.

#182 In nf-core/viralmetagenome;

· Joon-Klaps opened on May 21, 2025

Consider switching to CRAM where possible.

Status: Open.

#168 In nf-core/viralmetagenome;

· Joon-Klaps opened on Mar 21, 2025

Make viralmetagenome much more memory efficient

enhancementNew feature or requestNew feature or request

Status: Open.

#167 In nf-core/viralmetagenome;

· Joon-Klaps opened on Mar 21, 2025

Make custom annotation database using ncbi virus

documentationImprovements or additions to documentationImprovements or additions to documentation

websiteImprovements or feedback to the viralgenie websiteImprovements or feedback to the viralgenie website

Status: Open.

#137 In nf-core/viralmetagenome;

· Joon-Klaps opened on Jul 19, 2024

include option for protein clustering

enhancementNew feature or requestNew feature or request

Status: Open.

#135 In nf-core/viralmetagenome;

· Joon-Klaps opened on Jul 19, 2024