Initial release of nf-core/longraredisease, created with the nf-core template.

This release provides an end-to-end pipeline for comprehensive variant detection: structural variants (SV), single-nucleotide variants (SNV), copy-number variants (CNV), short tandem repeats (STR) and methylation, and clinical interpretation from long-read sequencing data (Oxford Nanopore and PacBio), aimed at rare disease diagnostics.

Added

• Read alignment to a reference genome with minimap2 (or winnowmap), and BAM processing/QC with samtools (sort, index, merge, stats, flagstat, idxstats).
• Multi-caller structural variant discovery using Sniffles, CuteSV and SVIM, with consensus merging via JASMINE.
• Haplotype-aware (phased) SV calling using LongPhase (phase and haplotag).
• Family/trio-based joint calling and de novo SV detection.
• Clinical SV annotation with AnnotSV (including annotation database installation) and SnpEff.
• Phenotype-driven SV prioritisation with SVANNA using HPO terms.
• Optional single-nucleotide variant calling with Clair3 and DeepVariant.
• Optional copy-number variant calling (Spectre/HiFiCNV), short-tandem-repeat genotyping (TRGT/Straglr) and methylation pileups with Modkit.
• VCF normalisation, filtering, merging and indexing with bcftools and tabix.
• Per-run reporting aggregated with MultiQC.