Fixed 🧰

• Fix singularity image pull tag for MAGeCKFlute (https://github.com/nf-core/crisprseq/pull/160)
• Escape dollar signs in containerOptions (https://github.com/nf-core/crisprseq/pull/163)
• Fix error in R script when adding patterns (https://github.com/nf-core/crisprseq/pull/170)
• Skip MAGeCKFlute when the function produces an error within the R package (https://github.com/nf-core/crisprseq/pull/170)

Highlights 🌟

This release adds FluteMLE for any MAGeCK MLE output as a visualisation and quality control. The users can now define their contrasts through a list which leads to MAGeCK MLE and BAGEL2 to be automatically run. Venn Diagrams also show the intersection between MAGeCK MLE and BAGEL2 when both tools are run. For the targeted analysis, several bugs have been fixed such as cutadapt on mixed paired- and single- end reads.

Added ➕

• Template update to 2.11.1 (#105)
• Added a csv input option for crisprcleanr (#105)
• Added a contrasts parameter so the pipeline automatically creates design matrices and MAGeCK MLE (#109)
• Added bowtie2 and three prime and five prime adapter trimming (#103 and #123)
• Added --day0_label and FluteMLE for MLE data #126
• Template update to 2.13.1 (#124)
• Metromap added in the docs (#128)
• Added MAGeCK count table in the multiqc (#131)
• Added additional plots to Tower output (#130)

Fixed 🧰

• Adapt cutadapt module to work with single-end and paired-end reads again (#121)
• Fix premature completion of the pipeline when paired-end reads were merged (#145)
• Create empty *-QC-indels.csv file if alignments not found. (#138)
• Fix --reference_fasta and --protospacer parameters (#144)

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)

v2.1.0 - Jamon Salas - [14.11.2023]

Highlights 🌟

This release includes new and improved documentation and reporting as well as a new analysis module for CRISPR/Cas9 screening : BAGEL2. The screening pipeline also now supports paired-end data.

Added ➕

• BAGEL2 modules which detect gene essentiality (#60)
• nf-validation
• New plots in the MultiQC for targeted screening (cutadapt module, read processing, edition, edition QC) (#74)

Fixed 🧰

• Change to process_high for the mageck mle module (#60)
• Fix paired-end samplesheet file for screening (#60)
• Summary processes don’t modify the input file anymore, allowing resuming these processes (#66)
• Do not stash unexistent files, use empty lists instead. Fixes AWS tests (#67)
• Rename process merging_summary to preprocessing_summary to improve clarity (#69)
• Fix modules BWA_INDEX and BOWTIE2_BUILD after module update, new versions accept a meta map (#76)
• Update targeted metromap (#78)

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.