[User Story] Consistent output formats - Githubissues

genomic-medicine-sweden / nallo

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

https://genomic-medicine-sweden.github.io/nallo/

MIT License

19 stars 4 forks source link

[User Story] Consistent output formats #64

Open fellen31 opened 7 months ago

fellen31 commented 7 months ago

Need

As a user, I want clear outputs. At the moment variant files are a mix of vcf and bcf, some indexed and some not, some compressed and some not.

Suggested approach

Standardise output variant files as compressed and indexed vcf (vcf.gz) files.

Can be closed when:

VCF.GZ

[x] TRGT singlesample
[x] GLNEXUS
- [x] #48
- [x] Multisample/case_id vcfs are annotated
[x] ECHTVAR_ANNO

BED.GZ

[x] Modkit
[x] Modkit haplotypes
[ ] (Dipcall)
- [ ] #187

TBI/CSI

[x] DeepVariant gVCF
[x] DeepVariant VCF
[x] HiFiCNV
[X] WhatsHap phase
[ ] (Dipcall)
- [ ] #187
[x] TRGT singlesample
[x] TRGT multisample
[X] Sniffles singlesample
[X] Sniffles multisample
[x] Modkit
[x] Modkit haplotypes

fellen31 commented 5 months ago

Let's break out file naming in a separate issue #154, since this will be more important closer to implementation.