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nf-core/crisprseq: Changelog

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

v2.3.0 - Lime Nightingale - [08.11.2024]

Added

  • Add module to classify samples by clonality (#178)
  • Add DrugZ, a module for chemogenetic interaction (#168)
  • Add Hitselection, a module for subsetting more likely true positives for KO screen based on the protein protein interaction (#191)
  • Make the use of gene essentiality module more user friendly and readable in the code (#194)

Fixed

  • Fix cutadapt 3' and 5' no such variable found bug (#187)
  • Fix design matrix bug that introduced dots instead of a hyphen (#190)
  • Make output of FluteMLE optional as when some pathways produce bugs some channels are then empty (#190)
  • Fix a typo in crisprcleanr/normalize, when a user inputs a file (#192)
  • Add Singularity and Docker tests in the CI, also fix any issues users had when running MAGeCKFlute with Docker or Singularity. (#214)

General

  • Run pipeline tests with docker, singularity and conda on CI (#185)

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.