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Review params and config naming

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#532 In nf-core/viralrecon;

· svarona opened on Oct 17, 2025

False “pycoqc” sample appears in MultiQC summary when no Nanopore samples pass filtering thresholds

bugSomething isn't workingSomething isn't working

Status: Open.

#530 In nf-core/viralrecon;

· svarona opened on Oct 16, 2025

Multi-batch data analysis with different library preparation methods

questionFurther information is requestedFurther information is requested

Status: Open.

#529 In nf-core/viralrecon;

· YangJingqii opened on Oct 15, 2025

Poor de novo assembly quality with frameshift errors

questionFurther information is requestedFurther information is requested

Status: Open.

#528 In nf-core/viralrecon;

· YangJingqii opened on Oct 15, 2025

Unexpected trimming patterns with cutadapt

bugSomething isn't workingSomething isn't working

Status: Open.

#527 In nf-core/viralrecon;

· YangJingqii opened on Oct 15, 2025

Questions about amplicon + fragmentation library workflows

questionFurther information is requestedFurther information is requested

Status: Open.

#526 In nf-core/viralrecon;

· YangJingqii opened on Oct 15, 2025

<code>--skip_ivar_trim</code> parameter appears to be ignored in amplicon mode

bugSomething isn't workingSomething isn't working

Status: Open.

#525 In nf-core/viralrecon;

· YangJingqii opened on Oct 15, 2025

Add freyja support for other organisms

bugSomething isn't workingSomething isn't working

Status: Open.

#519 In nf-core/viralrecon;

· svarona opened on Oct 9, 2025

· 

3.1

Update the metro map

bugSomething isn't workingSomething isn't working

Status: Open.

#517 In nf-core/viralrecon;

· svarona opened on Oct 8, 2025

Fixes before release

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#514 In nf-core/viralrecon;

· svarona opened on Oct 8, 2025

Add Amplicon coverage heatmap again to multiQC report

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#513 In nf-core/viralrecon;

· svarona opened on Oct 8, 2025

· 

3.1

Do not push Anaconda defaults channel

Status: Open.

#499 In nf-core/viralrecon;

· ammaraziz opened on May 7, 2025