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)