nf-core/crisprseq: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v2.2.1 Romarin Curie - patch - [23.07.2024]

Fixed

Fix singularity image pull tag for MAGeCKFlute (#160)
Escape dollar signs in containerOptions (#163)
Fix error in R script when adding patterns (#170)
Skip MAGeCKFlute when the function produces an error within the R package (#171)

v2.2.0 - Romarin Curie - [20.06.2024]

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)
More documentation for screening analysis. (#99)
Contrasts are now given under a different flag and MAGeCK MLE and BAGEL2 are automatically run instead of MAGeCK RRA. (#99)
Added cutadapt for screening analysis (#95)

Fixed

Fixed paired-end for screening analysis (#94)

v2.1.0 - Jamon Salas - [14.11.2023]

Added

Template update v2.9 (#52)
Use Channel.fromSamplesheet() from nf-validation to validate input sample sheets and create an input channel (#58)
BAGEL2 as a module which detects gene essentiality (#60)
Add custom plots to MultiQC report (cutadapt module, read processing, edition, edition QC) (#64)
Template update v2.10 (#79)

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)

Deprecated

v2.0.0 - Paprika Lovelace - [05.07.2023]

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]nf-core/test-datasets#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 (#50)
Fix id in crisprcleanr-normalize (#50)

v1.0 - Salted Hypatia - [02.02.2023]

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