Skip to content

Latest commit

 

History

History
147 lines (95 loc) · 9.44 KB

CHANGELOG.md

File metadata and controls

147 lines (95 loc) · 9.44 KB

Changelog

0.4.3 (2025-01-29)

Bug Fixes

  • swap activity threshold and all output file paths in qc_report rule (#172) (ff1b11c)

0.4.2 (2025-01-07)

Bug Fixes

  • swapped barcode output files (a851ad2)

0.4.1 (2025-01-06)

Bug Fixes

0.4.0 (2025-01-02)

⚠ BREAKING CHANGES

  • Major version change because of changes in config that are not backward compatible.

Features

  • Add performance tweaks for resource optimization in workflow rules (5ed1ef9)
  • Allowing also only FW reads with a UMI (56b2254)
  • Strand sensitive option (f315aab)
  • One DNA or RNA count file across multiple replicates (ccbacee)

0.3.1 (2024-12-17)

Bug Fixes

  • Wrong experiment count plots in QC report (#149) (d2be468)

0.3.0 (2024-11-20)

⚠ BREAKING CHANGES

  • versioned config (#140)

Features

  • versioned config (#140)
  • MAD outlier removal is completely removed (#140)
  • default is NO outlier detection (none is not present anymore) (#140)
  • global config is removed. splits moved now withing mapping in assignment (#140)

0.2.0 (2024-11-05)

⚠ BREAKING CHANGES

  • Support only snakemake >=8.24.1 (#130)
  • File output formats and locations changed
  • Normalization changed which may result in different outputs

Features

  • outlier removal methods (#132)
  • No min max length for bbmap. default mapq is 30. (#131)
  • IGVF outputs (#129)
  • Documentation improvements

Bug Fixes

0.1.1 (2024-09-30)

Bug Fixes

0.1.0 (2024-09-18)

First release of MPRAsnakeflow!

Feature highlights

  • Multiple assignment mapping strategies (BBMap, exact, bwa)
  • Optimized assignment for variants with BBMap
  • QC report for assignment and experiment workflow
  • Barcode count output
  • Snakemake 8 support
  • Extended documentation: https://mprasnakeflow.readthedocs.io

older development

⚠ BREAKING CHANGES

  • latest development for new release (#133)
  • pseudocounts where not used correctly when RNA or DNA set to 0
  • DNA and RNA join correction

Features

  • Add assignment_merge thread configuration (26e68c2)
  • better assignment BC statistics (00187e6)
  • configurable min mapping quality (28045ae)
  • extending figure width (8bf81c4)
  • faster design check (315b402)
  • fastq-join implementation (aaf5315)
  • latest development for new release (#133) (bdfc557)
  • make filtering consistent (5f7a4c5)
  • master variant table (6bda47c)
  • new final output file with merged replicates (66cf017)
  • only link assignment fasta when possible (d7d3822), closes #50
  • remove space, speedup BC extraction (70e9bd0)
  • replace merging by NGmerge (0aa8cad)
  • snakemake 8 compatibility (cf38ed9)
  • snakemake 8 ready with workflow profile (d637e1f)
  • statistic for assignment workflow (10c3b26)
  • using reverese compelment BCs (d009a6c)

Bug Fixes

  • batch size issue in sort (487ba8c)
  • correct use of assignment configs (58b64f1)
  • corrected qc_report_assoc (afb0127)
  • Detach from anaconda (#122) (16bcea2)
  • DNA and RNA join correction (7214743)
  • filter config (38ee37e)
  • issue with stats and asisgnment (d935fa1)
  • memory resources for bbmap (#123) (af93f58)
  • plots per insert only used last experiment. not all. (c2fd82b)
  • pseudocounts where not used correctly when RNA or DNA set to 0 (d2483f9)
  • remove illegal characters from reference (0ebee81)
  • rename barcoe output header (635f043)
  • rule make_master_tables fix (df42845)
  • statistic total counts (6381b92)
  • typo in report (ace8cca)
  • upgrade code to new pandas version (aaea236)
  • using correct threads (6dcad7d)
  • using multiple fastq inputs in counts (95935cf)