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BBDUK step takes forever to test - solutions?

questionFurther information is requestedFurther information is requested

Status: Open.

#13 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Aug 3, 2026

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bugSomething isn't workingSomething isn't working

Status: Open.

Task

#12 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Jul 29, 2026

Decide details of population-aware layer

Status: Open.

Task

#10 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Jul 29, 2026

Write GATK step according to Niaré et al. protocol

Status: Open.

Task

#8 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Jul 28, 2026

Create short read analysis track

Status: Open.

Task

#7 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Jul 28, 2026

Handle reference downloads

Status: Open.

Task

#6 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Jul 28, 2026

Integrate code from workflows/original_local.nf into workflows/pathogenepidemiology.nf

Status: Open.

Task

#5 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Jul 28, 2026

Decide on Long Read variant caller that supports polyploidy (fit for MOI analysis)

Status: Open.

Task

#4 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Jul 28, 2026

Update metromap

Status: Open.

Task

#2 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Jul 28, 2026

Support for samples with long and short read types

Status: Open.

Task

#1 In nf-core/pathogenepidemiology;

· BilalsGituation opened on Jul 28, 2026