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Replace RNAseq Human and mouse references
#10 · edmundmiller opened on Feb 8, 2024

Add species-specific parameters for splice-aware index generation (e.g., average exon length, sjdbOverhang)
nf-core/references#129 · opened on Oct 27, 2025
Add support for CHM13 Panel of normals
nf-core/references#126 · opened on Sep 11, 2025
Add support for snap-aligner index generation
Enhancement
nf-core/references#116 · opened on May 6, 2025
JSON schema: References
nf-core/references#107 · opened on Mar 25, 2025 · 1.0.0
Move annotation-cache in references
nf-core/references#104 · opened on Mar 24, 2025 · 1.1.0
Improve utils suborkflow usage
nf-core/references#103 · opened on Mar 21, 2025 · 1.0.0
Auto-generate params.yml for backwards compatibility for old rnaseq versions
nf-core/references#102 · opened on Mar 21, 2025 · 1.0.0
Figure out how to deal with a variable base_path
nf-core/references#101 · opened on Mar 21, 2025 · 1.0.0
Enhance schema to handle multiple files
nf-core/references#100 · opened on Mar 21, 2025 · 1.1.0
Add to schema all items from rnaseq
nf-core/references#99 · opened on Mar 21, 2025 · 1.0.0
Pipelines to support - 1.1.0
nf-core/references#98 · opened on Mar 21, 2025 · 1.1.0
Add EDAM ontologies
nf-core/references#85 · opened on Feb 24, 2025 · 1.0.0
Pipelines to support - 1.0.0
nf-core/references#83 · opened on Feb 13, 2025 · 1.0.0
Meta issue for Milestone 1.0.0
nf-core/references#82 · opened on Jan 30, 2025 · 1.0.0
Create chromap reference
Enhancement
nf-core/references#71 · opened on Jan 2, 2025 · 1.1.0
More meaningful name for field in input_schema.json, especially for the meta data
nf-core/references#65 · opened on Dec 12, 2024 · 1.1.0
Autogenerate index
nf-core/references#58 · opened on Dec 10, 2024 · 1.1.0
Autogenerate README
nf-core/references#57 · opened on Dec 10, 2024 · 1.1.0
Create Chromosomes/
nf-core/references#46 · opened on Nov 29, 2024 · 1.0.0
check out how sizes is different/similar to chr_chrom_len
nf-core/references#40 · opened on Nov 28, 2024 · 1.1.0
Add a Request a genome Issue template and add a reference PR template
nf-core/references#26 · opened on Nov 20, 2024 · 1.1.0
Enhance documentation
nf-core/references#18 · opened on May 17, 2024 · 1.0.0
1
Add tools from rnaseq
nf-core/references#16 · opened on Feb 27, 2024 · 1.0.0
Use topic channels for the modules in this workflow
nf-core/references#8 · opened on Feb 8, 2024 · 1.0.0
Setup actions
nf-core/references#7 · opened on Feb 8, 2024 · 1.1.0

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Issues

Issues

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

Add support for CHM13 Panel of normals

Add support for `snap-aligner` index generation

JSON schema: References

Move annotation-cache in references

Improve utils suborkflow usage

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

Figure out how to deal with a variable base_path

Enhance schema to handle multiple files

Add to schema all items from rnaseq

Pipelines to support - 1.1.0

Add EDAM ontologies

Pipelines to support - 1.0.0

Meta issue for Milestone 1.0.0

Create chromap reference

More meaningful name for field in input_schema.json, especially for the meta data

Autogenerate index

Autogenerate README

Create Chromosomes/

check out how sizes is different/similar to chr_chrom_len

Add a Request a genome Issue template and add a reference PR template

Enhance documentation

Add tools from rnaseq

Use topic channels for the modules in this workflow

Setup actions