Neon tetra

nf-core/pacvar 1.1.0 - Neon tetra

nf-core/pacvar 1.1.0 expands the WGS workflow with major new PacBio long-read analysis capabilities, including copy number variant calling (hificnv), optional sawfish structural variant calling (sawfish), CpG methylation profiling (pb-CpG-tools), Fiber-seq processing (fibertools-rs), and VEP annotation for SNVs, indels, SVs, and CNVs (ensemblvep).

This release also adds optional fail BAM support (pbmerge) for the repeat workflow, including HiFi and fail BAM merging after mapping. The pipeline has been refreshed to nf-core/tools 4.0.2, with updated core nf-core modules, MultiQC integration, container configuration files, test profiles, documentation, and schema support.

Highlights include:

• New HiFiCNV copy number variant calling support with hificnv
• Optional sawfish SV and CNV calling
• CpG methylation profiling with pb-CpG-tools
• Fiber-seq support with fibertools-rs
• VEP annotation for SNVs, indels, SVs, and CNVs
• Optional VEP cache download support
• Optional fail BAM handling in the repeat workflow
• Updated nf-core template 4.0.2
• Updated tool versions, including DeepVariant, GATK4, pbsv, TRGT, MultiQC, samtools, bcftools, and others

This release substantially broadens pacvar’s PacBio variant discovery and annotation functionality while keeping the workflow aligned with current nf-core infrastructure.

Thanks to everyone who contributed to and reviewed this release.

Contributors: @chaochaowong, @stvdsomp, @tanyasarkjain

Reviewers: @vagkaratzas, @tanyasarkjain, @maxulysse, @nvnieuwk, @pinin4fjords, @YiJin-Xiong, @mashehu, @SPPearce