2.1.3

Fixes

• ashleys-qc sklearn new version compatibility
• Cleaning

2.1.2

Features

• mm10 assembly support for all the steps
• UCSC compatible .gz file automatically generated

Bug fixes

• Removing some unnecessary print commands in regenotype.R
• Cleaning up some Arbi scripts

Commits

• 538fdf0: 2.1.2: fix docker memory space limit (Thomas Weber) #44

What's Changed

• 2.1.2: Docker fix by @weber8thomas in #43
• 2.1.2: fix docker memory space limit by @weber8thomas in #44

Full Changelog: 2.1.1...2.1.2

2.1.1

Features

• multistep normalisation for SV calling (T2T, hg19 assemblies GC matrices added)

Bug fixes

• Normalisation behavior and conditional execution change
• Normalisation R script change to only apply scalar if hgsvc_based_normalisation enabled, only blacklisting otherwise

Full Changelog: 2.0.1...2.1.1

2.0.1

Bug fixes

• ArbiGent all SV genotyping fixes
• Compatibility with all samples name, remove HGSVC regex
• Add ipynb for publication purpose

Commits

• 4680e13: Revert "Arbi debug" (Thomas Weber) #37

2.0.0

Features

• scNOVA binding

Details

Versioning harmonisation
Fixing BSgenome install issue (trial 4)
Fixing dataframe configuration issue related to selected cells to be used in scNOVA
Functional version, optimisations are still required
Done:

• Docs
• Zenodo upload
• Conda envs
• Path update to be compliant to mosaicatcher standards
• Code optimisation (DL parallelisation instead of sequential steps)
• deeptools to bedtools + parallelisation followed by aggregation
• Prefix path inside R & perl scripts

Full Changelog: 1.9.1...2.0.0

1.9.1

Features

• ArbiGent integration update
• publishdir for ashleys

Fixes

• normalization fix

Full Changelog: 1.9.0...1.9.1

1.9.0

Features

• ArbiGent integration

Full Changelog: 1.8.6...1.9.0

1.8.5

Features

• bam/selected folder system update
• report captions update
• blacklist files for T2T + hg19

@weber8thomas in #22

Full Changelog: 1.8.4...1.8.5

1.8.4

Features

• fixing BAM input issue
• input_bam_legacy mode (bam/selected)
• ashleys_threshold parameter

@weber8thomas in #21

Full Changelog: 1.8.3...1.8.4

1.8.3

Commits

• 1cba402: Docs update (Thomas Weber) #20

What's Changed

• Minor update, dedicated env for plot-clustering.R by @weber8thomas in #19
• Docs update by @weber8thomas in #20

Bugs

• Synchronize versions between mosaicatcher-pipeline and asheys-qc pipeline using versions in config and Snakefile

Full Changelog: 1.8.2...1.8.3