Refactor call repeat expansions

genomic-medicine-sweden / nallo

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

MIT License

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Closed fellen31 closed 18 hours ago

fellen31 commented 7 months ago

Refactor repeat calling workflow to bring code in sync and up to par with other nf-core pipelines.

[x] Rename repeat_analysis to call_repeats, call_str(s), str_calling or similar, align with conf and output directories
[ ] #139
[x] Replace bcftools index with bcftools merge --write-index
[ ] Add tbi output to call repeat expansions
[x] #414

fellen31 commented 18 hours ago

These issues can be tracked separately.