Version history

This is a patch release

What’s Changed

  • Add pipeline schema
  • Update environment to fix broken dependancies by @maxibor in #50

Full Changelog: 1.1…1.1.1

Changes since version 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  • Remove outdated scripts #14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
  • coproID is now published in PeerJ

coproID release 1.0

coproID is a pipeline I originally developped outside of nf-core to perform the host identification of archaelogical faeces using endogenous DNA content and machine learning on microbiome compositon. I adapted it to nf-core recently, following the hackaton in Tubingen.

coproID contains both published external softwares, homecooked package (sourcepredict), as well as custom python scripts.

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