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coproID v1.0 - Dioptre Walrus
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@maxibor maxibor released this 29 Apr 14:55
· 129 commits to master since this release
1.0
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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
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