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v2.2.0 - Romarin Curie
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@LaurenceKuhl LaurenceKuhl released this 20 Jun 15:03
· 269 commits to master since this release
2.2.0
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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)
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