Issues · genomic-medicine-sweden/nallo · GitHub

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Rename preset `pacbio` to `sequel_II` and use `pacbio` as default instead of `revio`

needs refinement

#1039

· fellen31 opened

on Apr 24, 2026

On PRs to master from dev, warn about not squash merging

#1036

· fellen31 opened

on Apr 24, 2026

Add Kivvi

needs refinement

#1028

· fellen31 opened

on Apr 23, 2026

Move Alignment into own subworkflow

#1027

· Schmytzi opened

on Apr 23, 2026

·

Add support for mapped BAMs as input

#1026

· Schmytzi opened

on Apr 22, 2026

`mitochondrial_caller = deepvariant` does not work when `snv_caller = sentieon`

#1023

· alkc opened

on Apr 10, 2026

Speed up stub tests

#1022

· fellen31 opened

on Apr 2, 2026

·

Migrate `vcf_concat_sort_variants` to workflow outputs

#1014

· fellen31 opened

on Mar 31, 2026

Migrate `whatshap` to workflow outputs

#1015

· fellen31 opened

on Mar 31, 2026

Migrate `vcf_concat_norm_variants` to workflow outputs

#1013

· fellen31 opened

on Mar 31, 2026

Migrate `utils_nfcore_nallo_pipeline` to workflow outputs

#1012

· fellen31 opened

on Mar 31, 2026

Migrate `scatter_genome` to workflow outputs

#1010

· fellen31 opened

on Mar 31, 2026