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--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 BWA-FastAlign as a more efficient alternative to BWA-MEME

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#865 In nf-core/raredisease;

· fellen31 opened on May 31, 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

Allow usage of CADD prescored files

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#862 In nf-core/raredisease;

· fellen31 opened on May 29, 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

run_mt_for_wes and skip_split_multiallelics swapped in workflow

bugSomething isn't workingSomething isn't working

Status: Open.

#854 In nf-core/raredisease;

· benstory opened on May 22, 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