Gagneurlab Drop Versions Save

• fixes the FRASER version to 1.99.3 commit d6a422c to ensure reproducibility
• fixes the OUTRIDER version to 1.20.1
• fixes certain scripts affected by a snakemake update

Fixes a bug when compiling the aberrant splicing results.

Fixes issues with having only 1 internal sample. Simplifies the counting Summary html in the aberrant splicing module.

• small bugfix in the Aberrant Splicing Counting Summary Script when providing only 1 external sample

• Supports FRASER 2.0, an improved version that uses the Intron Jaccard Index as its single splice metric
• Allows to provide lists of genes to test during FDR correction in addition to the transcriptome-wide FDR across all expressed genes

What's Changed

• Bug Fixes in MAE
• yieldSize and dnaRnaMatchCutoff config values
  • yieldSize: allows for memory consideration in VCF and BAM file processing
  • dnaRnaMatchCutoff: sets the threshold for MAE sample matching
• Summary edits to aberrantSplicing

Full Changelog: https://github.com/gagneurlab/drop/compare/1.2.3...1.2.4

• Fix AE Export #353
• Multiple bug fixes #350, #364, #378
• Simplified QC reporting #361, #390
• Improve Reporting/Summaries #376, #384
• Match documentation and defaults in config: https://github.com/gagneurlab/drop/commit/45075c474452fa429299c3f65cb4858671f06020

Full Changelog: https://github.com/gagneurlab/drop/compare/1.2.2...1.2.3

Fixes a bug in the aberrant expression module when external counts are not provided.

Full Changelog: https://github.com/gagneurlab/drop/compare/1.2.1...1.2.2

Full Changelog: https://github.com/gagneurlab/drop/compare/1.2.0...1.2.1

fix for Bioconda test

What's Changed

• Dev by @nickhsmith in https://github.com/gagneurlab/drop/pull/336

Full Changelog: https://github.com/gagneurlab/drop/compare/1.2.0...1.2.1

What's Changed

• Update to MAE filter scripts by @nickhsmith in https://github.com/gagneurlab/drop/pull/320
• Merge external splicing counts by @c-mertes in https://github.com/gagneurlab/drop/pull/247
• Gatk updates by @nickhsmith in https://github.com/gagneurlab/drop/pull/326
• add warning for no results by @nickhsmith in https://github.com/gagneurlab/drop/pull/328
• RNA variant calling by @nickhsmith in https://github.com/gagneurlab/drop/pull/325

Addition of the rnaVariantCalling module and inclusion of external splice counts for the aberrantSplicing module

Full Changelog: https://github.com/gagneurlab/drop/compare/1.1.4...1.2.0