DROP 1.2.0

What's Changed

• Update to MAE filter scripts by @nickhsmith in #320
• Merge external splicing counts by @c-mertes in #247
• Gatk updates by @nickhsmith in #326
• add warning for no results by @nickhsmith in #328
• RNA variant calling by @nickhsmith in #325

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

Full Changelog: 1.1.4...1.2.0

DROP 1.1.4

What's Changed

• fix dict creation extension matching by @nickhsmith in #312
• Mae fasta fix by @nickhsmith in #313
• Version bump by @nickhsmith in #314
• Dev by @nickhsmith in #315

Full Changelog: 1.1.3...1.1.4

DROP 1.1.3

Bug fix for import counts for the aberrantExpression module.
removed MAE checks and installs when MAE module is turned off using config run: false

small bugs fixes

What's Changed

• Update filterSNVs.sh by @nickhsmith in #253
• Ranges by @vyepez88 in #277
• Qc improve by @vyepez88 in #279
• Mae hpo fix by @vyepez88 in #281
• update conda to mamba install by @nickhsmith in #289
• Separate rvc by @nickhsmith in #221
• Revert "Separate rvc (#221)" by @nickhsmith in #302
• Import counts fix by @nickhsmith in #303
• Pre checks by @nickhsmith in #305
• merge counts fixed and gtex hg38 added by @vyepez88 in #304
• bump version by @nickhsmith in #306
• Dev by @nickhsmith in #307

Full Changelog: 1.1.2...1.1.3

DROP 1.1.2

What's Changed

HPO fixes
MAE allele frequency fixes
MAE filterSNV fixes
Updated documentation and versions

• Dev by @nickhsmith in #290
• Dev by @nickhsmith in #292

Full Changelog: 1.1.1...1.1.2

DROP 1.1.1

DROP 1.1.1

Update to version 1.1.1 (#273)

Major changes included in this update are:

• Correct MAE filtering (#241)
• Simplify FRASER results (#263)
• Update documentation

On top of this many small bug-fixes are included:

#249 #254 #256 #258 #262 #265 #271

Full Changelog: 1.1.0...1.1.1

DROP 1.1.0

Update to version 1.1.0 (#229)

Major changes included in this update is:

• adapt to new snakemake version (#208)
• Speedup CI (use micromamba, #218)
• Add HTML cutoff for results (#217)
• Separate modules (#209)
• Update documentation (#228)

On top of this many small bug-fixes are included:

• #175 #192 #198 #231
• Simplify result reporting

1.0.5

• simplify results output @vyepez88
• add MAE error messages for empty output @mumichae
• more robust dependency graph generation @nickhsmith @mumichae

DROP 1.0.4

• add possibility to work with different reference genome files
• annotate aberrant splicing results using the gtf file
• better handling of dependencies
• improved drop update process
• minor bug fixes

1.0.3

• Annotation of aberrant splicing results now takes the gene names from the provided gtf file
• Added the genomes GRCh37 and GRCh38 to count split reads
• Continuous integration through GitHub actions
• Minor bug fixes

Bump version: 1.0.1 -> 1.0.2

• fix pipeline when no import count matrix in sample annotation #114

• refactored config parsers by submodule

• update to FRASER 1.2.0 @c-mertes

• update aberrant splicing export @c-mertes

• local loading of HPO file if present @vyepez88

• fixed buggy file extension when saving ods @jemten

• check R package version with reinstall