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Handle reads with no quality scores

Status: Open.

#203 In nf-core/pathogensurveillance;

· zachary-foster opened on Jun 2, 2026

Handle SRA accessions that dont have data assocaited with them

Status: Open.

#201 In nf-core/pathogensurveillance;

· zachary-foster opened on Apr 30, 2026

Modifications to the dashboard report layout

Status: Open.

#199 In nf-core/pathogensurveillance;

· zachary-foster opened on Apr 8, 2026

Add warning when the user defined references that are not used.

Status: Open.

#198 In nf-core/pathogensurveillance;

· zachary-foster opened on Feb 27, 2026

Add DOI to nextflow.config

bugSomething isn't workingSomething isn't working

Status: Open.

#196 In nf-core/pathogensurveillance;

· FriederikeHanssen opened on Feb 16, 2026

The bakta database dowloaded by conda and docker are not compatible

bugSomething isn't workingSomething isn't working

Status: Open.

#191 In nf-core/pathogensurveillance;

· zachary-foster opened on Jan 28, 2026

·  

1.2.0

Allow sample IDs to be numbers

Status: Open.

#189 In nf-core/pathogensurveillance;

· zachary-foster opened on Jan 26, 2026

ERROR ~ Error executing process > 'NFCORE_PATHOGENSURVEILLANCE:PREPARE_INPUT:SAMPLESHEET_CHECK (input.csv)'

Status: Open.

#184 In nf-core/pathogensurveillance;

· lukaskon opened on Oct 9, 2025

Find assemblies faild with test run

bugSomething isn't workingSomething isn't working

Status: Open.

#183 In nf-core/pathogensurveillance;

· alarawms opened on Sep 7, 2025

No need to have the nft-utils-0.0.3.jar file

Status: Open.

#182 In nf-core/pathogensurveillance;

· maxulysse opened on Sep 4, 2025

Investigate Ariba for detecting genes from raw reads

Status: Open.

#181 In nf-core/pathogensurveillance;

· zachary-foster opened on Aug 19, 2025

Try using gtExtras for tables in report

enhancementNew feature or requestNew feature or request

Status: Open.

#179 In nf-core/pathogensurveillance;

· zachary-foster opened on Jul 9, 2025

·  

1.1.0