Add longphase #388
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Add longphase #388
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rannick
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Sep 25, 2024
README.md
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| --fasta <reference.fasta> \ | ||
| --outdir <OUTDIR> | ||
| --preset revio \ | ||
| --fasta reference.fasta \ |
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| --fasta reference.fasta \ | |
| --fasta reference.fasta \ |
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I like formatting the options within brackets better as it highlights what the user has to provide
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I'll change it back!
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Thanks @rannick! |
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This PR closes #291, by adding LongPhase as the default phaser. This reduces the runtime of the pipeline by ~3-4 hours, while producing comparable results. Both whatshap and HiPhase are kept for now, because they each have their own strengths that have not been properly examined (for example whatshap pedigree phasing).
Co-phasing of SNVs and SVs with HiPhase is removed in this PR, since that workflow was not being tested, and was not working.
All SV-callers VCFs outputs are not similar, and the only really supported caller for HiPhase is pbsv. Other callers might require modifications to the VCF, which adds complexity and needs to be investigated further. Perhaps we should always run multiple SV-callers to support this.
I've added an issue to support co-phasing of SNVs and SVs with LongPhase and/or HiPhase (#389) to track the progress of (re-implementing) co-phasing.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).