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Creates and uses HISAT2_EXTRACTSPLICESITES when hisat2_extractsplicesites not specified

bugSomething isn't workingSomething isn't working

Status: Open.

#130 In nf-core/references;

· anilthanki opened on Oct 31, 2025

Add species-specific parameters for splice-aware index generation (e.g., average exon length, sjdbOverhang)

enhancementNew feature or requestNew feature or request

Status: Open.

#129 In nf-core/references;

· anilthanki opened on Oct 27, 2025

Add support for CHM13 Panel of normals

enhancementNew feature or requestNew feature or request

Status: Open.

#126 In nf-core/references;

· ljwharbers opened on Sep 11, 2025

Add support for snap-aligner index generation

enhancementNew feature or requestNew feature or request

Status: Open.

Enhancement

#116 In nf-core/references;

· matthdsm opened on May 6, 2025

JSON schema: References

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#107 In nf-core/references;

· jen-reeve opened on Mar 25, 2025

·  

1.0.0

Move annotation-cache in references

enhancementNew feature or requestNew feature or request

Status: Open.

#104 In nf-core/references;

· maxulysse opened on Mar 24, 2025

·  

1.1.0

Improve utils suborkflow usage

enhancementNew feature or requestNew feature or request

Status: Open.

#103 In nf-core/references;

· maxulysse opened on Mar 21, 2025

·  

1.0.0

Auto-generate params.yml for backwards compatibility for old rnaseq versions

enhancementNew feature or requestNew feature or request

Status: Open.

#102 In nf-core/references;

· maxulysse opened on Mar 21, 2025

·  

1.0.0

Figure out how to deal with a variable base_path

enhancementNew feature or requestNew feature or request

Status: Open.

#101 In nf-core/references;

· maxulysse opened on Mar 21, 2025

·  

1.0.0

Enhance schema to handle multiple files

enhancementNew feature or requestNew feature or request

Status: Open.

#100 In nf-core/references;

· maxulysse opened on Mar 21, 2025

·  

1.1.0

Add to schema all items from rnaseq

enhancementNew feature or requestNew feature or request

Status: Open.

#99 In nf-core/references;

· maxulysse opened on Mar 21, 2025

·  

1.0.0

Pipelines to support - 1.1.0

enhancementNew feature or requestNew feature or request

Status: Open.

#98 In nf-core/references;

· maxulysse opened on Mar 21, 2025

·  

1.1.0