v1.0.0 - Telperion

Version 1.0.0 ! The pipeline has got all the features it was intended to have, as discussed through the GSoC 2025 edition.

Enhancements & fixes

• Update BCFtools to version 1.22.1
• Use BCFtools to produce and plot VCF stats
• Added options to pass parameters to VCFtools and BCFtools
• Support BCF files
• Multiple options to define allele frequencies when computing ROH
• Support multi-sample VCF file
• Can use pre-existing Tabix index of the input VCF files
• Wrote documentation and a pipeline diagram
• Updated the underlying nf-core template to v4.1.0 and bumped up the nf-schema plugin to ensure
  seamless compatibility with Nextflow 26.04

Parameters

This release with the following initial parameters:

Old parameter	New parameter
	--vcftools_filter
	--site_pi_filter
	--het_filter
	--snp_density_filter
	--af_filter
	--indel_len_filter
	--roh_filter
	--af_tag
	--af_default_value
--roh_threshold

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only Docker or Singularity containers are supported, conda is not supported.

Dependency	Old version	New version
Matplotlib		3.10.6
Tectonic		0.15.0
Pigz		2.8
HTSlib	1.21	1.22.1
BCFtools	1.21	1.22

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.