Skip to content

Release notes

Change log

v1.2.2 Unreleased

  • Cleanup of majiq's workflow
  • Update the docs to clarify how to save containers at a user-specified location
  • Force chr column to be of type chr in baltica/parse_junctionseq_output.R

v1.1.2 Unreleased

  • Add support to unstranded RNA-seq data
  • Add scripts for benchmark
  • Add a new configuration bind_paths that allow integrating bam files from different projects

v1.1.1 July 23, 2021 (released in September 7 2021)

  • Add rmats workflow
  • Add scrips for parsing for rmats and updated analysis to support the method
  • Create the benchmark with the ONT Nanopore-seq
  • Update benchmaks, included difference comparison for SIRV benchmark
  • Split annotation and AS type assigment functions
  • Update baltica table algorithm
  • Add support for singularity container via snakemake, with container recipes baltica qc config.yaml --use-singularity
  • Add parsing method for gffcompare tracking output
  • Update configuration file to expose important parameters from the DJU methods
  • Add end-to-end analysis with baltica all config
  • Experiment with meta-score (gradient boosted trees)
  • Add baltica report and improved on report summaries
  • Add orthogonal dataset use-case, to integrate third generation sequencing to the baltica table
  • Change strand parameter to "fr-firststrand": "reverse", "fr-secondstrand": "forward" or unstranded, fix error in rmats strand

v1.0 September 17, 2020

  • Add is_novel column, indication introns not into the reference annotation
  • Remove unitended columns (X1, ...) from the report

v1.0 - July 23, 2020

  • First public release comprises of DJU methods Leafcutter, Junctionseq and Majiq. Stringtie for de novo transcriptomics assembly. FastQC and MultiQC (#1).