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sanger-tol/variantcomposition: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[0.2.0] - Telperion - [2025-xx-xx]

Enhancements & fixes

  • Update BCFtools to version 1.22.1
  • Use BCFtools to produce and plot VCF stats

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
Tar 1.34
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.

[0.1.0] - Laurelin - [2025-09-04]

Initial release of sanger-tol/variantcomposition, created with the nf-core template version 3.3.1.

Enhancements & fixes

  • Use Bgzip to index the VCF files
  • Use VCFtools to calculate SNP density
  • Use VCFtools to create InDel-sizes distribution in histogram
  • Use VCFtools to calculate per-site (base) nucleotide diversity
  • Use VCFtools to calculate heterozygosity
  • Use VCFtools to calculate allele frequency
  • Use BCFtools to generate ROH

Parameters

This release with the following initial parameters:

Old parameter New parameter
--input
--include_positions
--exclude_positions
--snp_density_window
--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
HTSlib 1.21
BCFtools 1.21
VCFtools 0.1.16

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.