Version history

v2.1.1 - Jamon Salas - patch - [14.12.2023]

Added

  • Update all modules to the last version in nf-core/modules (#92)
  • Added cutadapt for screening analysis (#95)

Fixed

  • Fixed paired-end for screening analysis (#94)

v2.0.0 - Paprika Lovelace - [05.07.2023]

Highlights 🌟

This release includes a whole new analysis type : functional genomics screenings (activation, interference or knock outs screens). For CRISPR-targeting, UMIs clustering is now supported. The usage of the pipeline now includes the flag --analysis <screening,targeted> to allow the user to indicate which analysis they would like to run.

Added ➕

  • Crisprseq screening analysis : mageck mle, mageck rra, mageck count and crisprcleanr-normalize (#22)
  • Add new parameter --analysis to select analysis type (screening/targeted) (#27)
  • Tests to run screening analysis (#926)
  • Metro map for targeted analysis (#35)
  • Add new parameters --reference and --protospacer (#45)
  • Add UMI clustering to crisprseq-targeted (#24)
  • Template update v2.8 (#21)

Fixed 🧰

  • Fix warning “module used more than once” (#25)
  • Remove profile aws_tower, update from nf-core/tools v2.9 to make full tests pass (#50)
  • Remove quay.io from all containers (#50)
  • Fix resources on test screening full (#56)
  • Fix id in crisprcleanr-normalize (#56)

Initial release of nf-core/crisprseq, created with the nf-core template.