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nf-core/coproid: Changelog

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

v2.0.1 - 06/02/2026

Changed

  • Fixed the Nextflow version badge to ≤24.10.5
  • Added some extra information to the README about running the pipeline offline and on HPC with container restrictions
  • Updated nf-core/tools to the latest version (by @jfy133)

Dependencies

Tool Old Version New Version
nf-core/tools 3.2.0 3.5.2

v2.0.0 - 22/05/2025

nf-core/coproid v2.0 is based on nf-core DSL2 template. This release is a complete rewrite of the original nf-core/coproid pipeline, originally written in Nextflow DSL1. It also includes new features, and/or updated tools.

Changed:

  • DSL2 rewrite
  • fastp replaced AdapterRemoval for read quality trimming/merging.
  • sam2lca is now used for computing the endogenous host DNA quantity, instead of custom python scripts, allowing for handling more flexibly test host genomes.
  • Pipeline reporting is now performed using Quarto, instead of Jupyter notebook
  • Minor JSON schema updates

New

  • aDNA damage testing using PyDamage
  • Interactive plots in report
  • Unit testing of most modules in the pipeline.

Added

Fixed

Dependencies

Deprecated

v1.1.1

Fixed

  • Fix #37 with conda environment and docker container update

v1.1.0

  • Update mapped basepair count to be quicker and include it in report #14
  • Remove outdated scripts #14
  • Update logo to match font #13
  • Update Sourcepredict to version 0.4 and reflect new parameters in coproID #19 e4afca7 c2d4164
  • Changed bedtools bamtofastq to samtools fastq e4afca7
  • Fixed column names in report (PC* to DIM*) e4afca7
  • Update README to inlude Zenodo badge, Quick start, contributor section, and tools references. 9874ae8 e85988b
  • Update documentation bedfdde
  • Update Nextflow minimum version to 19.04.0 44999fd
  • Update travis for more recent nextflow requirements 1e3e454
  • Adapt coproID to nf-core tools 1.8 release #21
  • Add social preview image #22
  • Fix Kraken2 segmentation error #26
  • Update to nf-core tools 1.9 release, and doc for new version of sphinx #27

v1.0.0 - 2019-04-26

Initial release of nf-core/coproid, created with the nf-core template. Adapting CoproID to nf-core template

Improvements over coproID version 0.6

  • Support for 3 organism comparison
  • Adding sourcepredict
  • Updating reports to have interactive plotting
  • Updated to use Kraken2 instead of Kraken1
  • Adding docker

Adaptions to port to nf-core

  • Major redefinition of the channels creation to adapt to iGenomes and profiles
  • Added and adapted all the nf-core boilerplate code for support of configs and containers
  • Improved documentation