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CADD 1.7.3 module update missing in CHANGELOG for v3.0.0

Status: Open.

#888 In nf-core/raredisease;

· fellen31 opened on Jun 18, 2026

--hisat2 parameter is declared but never used (genome HISAT2 index always rebuilt)

Status: Open.

#882 In nf-core/raredisease;

· apolitics opened on Jun 14, 2026

Update to VEP 116.0

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#872 In nf-core/raredisease;

· fellen31 opened on Jun 10, 2026

Consider adding riker as a faster and more efficient alternative to Picard QC metrics

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#871 In nf-core/raredisease;

· fellen31 opened on Jun 10, 2026

Non-stub pipeline level tests

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#869 In nf-core/raredisease;

· fellen31 opened on Jun 2, 2026

Unsafe pattern in annotate_genome_snvs?

bugSomething isn't workingSomething isn't working

Status: Open.

#868 In nf-core/raredisease;

· fellen31 opened on Jun 1, 2026

Consider adding FastDup as a faster and more efficient alternative to MarkDuplicates

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#864 In nf-core/raredisease;

· fellen31 opened on May 31, 2026

Combine sample_id_map with input sampesheet

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#861 In nf-core/raredisease;

· fellen31 opened on May 29, 2026

Add pipeline level test where sample_id_map is not null

Status: Open.

#860 In nf-core/raredisease;

· fellen31 opened on May 29, 2026

Skip tools eklipse causing error when using -profile test_singleton

bugSomething isn't workingSomething isn't working

Status: Open.

#852 In nf-core/raredisease;

· zoeward-nz opened on May 21, 2026

nfcore/dev: CI/CD fails due to saltshaker snapshot diff

bugSomething isn't workingSomething isn't working

Status: Open.

#845 In nf-core/raredisease;

· torbjorgen opened on May 8, 2026

SVDB_MERGE: Failure on -profile test,docker

bugSomething isn't workingSomething isn't working

Status: Open.

#844 In nf-core/raredisease;

· torbjorgen opened on May 8, 2026