History

The changelog for MPRAsnakeflow is included below. It provides a detailed history of changes, updates, and improvements made to the project.

Changelog

0.7.0 (2026-06-03)

⚠ BREAKING CHANGES

  • assignment: cigar filtering for BWA and optional length filter (#273)

Features

  • assignment: cigar filtering for BWA and optional length filter (#273) (f8d51e0)

  • experiment: :sparkles: NGmerge for paired-end BC reads merging (#270) (68b5175)

Bug Fixes

  • duplicated rule experiment_counts_noUMI_merge_NGmerge (defa204)

Documentation

  • :memo: Adding example using data GEO:GSE306816 (5f4595b)

  • add GSE293036 example with correct FASTQ file names (#269) (ff607b5)

  • Added Zahm and KopliK examples - GSE271608 and GSE307247 (#275) (bb0292b)

  • fixing typos (6c4f52a)

  • overview page of examples and more examples (#272) (136d681)

  • Potential fix for pull request finding (a067b86)

  • sphix compilation (803594e)

  • typo fixes (5e491a8)

  • typo fixes and build cleanup (d44e87d)

  • update example config (daf884a)

0.6.5 (2026-05-06)

Bug Fixes

  • experiment: :bug: Fix input of rul experiment_preprocessing_trim_reads (#267) (47c796d)

0.6.4 (2026-05-06)

Bug Fixes

  • experiment: :bug: Fix error in check if trimming is needed (625c6ea)

0.6.3 (2026-05-05)

Bug Fixes

  • assignment: :tada: Using mem_mb resoucres for bbmap for snakemake >=9.20.0 compatibility (8ddd146)

0.6.2 (2026-04-23)

Bug Fixes

  • experiment: :ambulance: Do not allow _ or . in Condition or Replicate (b4f3234)

  • experiment: :fire: split_numer was used wrongly when multiple experiments where defined (370411f)

0.6.1 (2026-04-22)

Features

  • Assignment: Long read support with pbmm2 mapper (#247) (759453d)

  • experiment: :rocket: FWD/REV(/UMI) reads can be splitted into n files before merging (#249) (a41e13e)

Bug Fixes

  • experiment: :bug: Missing getReads function for correct trimming (440e7bd)

0.6.0 (2026-02-11)

⚠ BREAKING CHANGES

  • renaming output files to use dots instead as undersocres a file separators (#239)

  • assignment adapter removal by length. Assignment config, adapter and forward read (now FWD), changed (#237)

Features

  • assignment adapter removal by length. Assignment config, adapter and forward read (now FWD), changed (#237) (521735e)

  • configurable bwa (#244) (9550e22)

  • enhance trimming functionality and update config schema for adapter specifications (798cebb)

  • experiment adapter trimming and option to do BC (also UMI if available) selection from end of the read (FWD only) (#238) (04dd683)

  • fastq-join as option for merging reads (assignment workflow) (#243) (093e288)

  • implement adapter trimming functionality in experiment rules (9fd32ce)

Bug Fixes

  • correct parameter name in check_version function (7cd50a5)

  • snakemake reverted default value handling (#236) (fa5109b)

Code Refactoring

  • renaming output files to use dots instead as undersocres a file separators (#239) (0546082)

0.5.9 (2026-01-07)

Bug Fixes

0.5.8 (2025-10-27)

Bug Fixes

  • fixed various small bugs in mapping_bbmap.smk, attachBCToFastQ.py, quality_metrics.py (#220) (90380be)

  • issues in assignment check (#230) (f25b74f), closes #217 #221

  • workaround for default values in schema files when using remote exec (#228) (261bcb3)

0.5.7 (2025-10-06)

Bug Fixes

0.5.6 (2025-10-01)

Features

  • bwa additional filtering (#216) (9c81cfd)

  • assignment workflow: allow single end reads (FW only) (#218) (9c81cfd)

0.5.5 (2025-09-17)

Bug Fixes

  • removed hard-coded barcode length (20) in hybrid reads (assignment workflow) (#213) (1d89232)

0.5.4 (2025-06-25)

Features

  • 5’ and 3’ adapter removal option using cutadapt (#207) (a36c023)

Bug Fixes

  • qname (read name) length cannot be longer than 255 characters (#206) (46fe287)

0.5.3 (2025-05-13)

Bug Fixes

  • channel order has to be correct for newer samtools (d0ada2b)

0.5.2 (2025-05-13)

Bug Fixes

  • set htslib and samtools version to 1.21 to avoid ncurses lib clashes (cb59bd4)

0.5.1 (2025-05-12)

Bug Fixes

  • missed config version upgrades (df5391a)

0.5.0 (2025-04-09)

⚠ BREAKING CHANGES

  • restructure folders and conda env import. Renaming of rules. Old SLURM ressoucres have to be updated

Features

  • IGVF qc metrics report (3ec5012)

  • Quality metric json file (for IGVF) and included within QC report (981baac)

Bug Fixes

Code Refactoring

  • restructure folders and conda env import. Renaming of rules. Old SLURM ressoucres have to be updated (f21cdca)

0.4.7 (2025-04-03)

Bug Fixes

  • assignment barcode counting (9584802)

  • merge.label.py does not return pseudocounts in barcode file (#187) (023110a)

  • report also barcodes that are lower than the min barcodes. (90f1b14), closes #185

  • issues on some environments while plotting with statistic_assignment.R (#186)

0.4.6 (2025-02-26)

Bug Fixes

  • revert v0.4.5. The fix was already implemented within the common.smk file (7997440)

0.4.5 (2025-02-24)

Bug Fixes

  • change the length of the sequence we want to check in the attach_sequence case (#177) (e3db5cf)

0.4.4 (2025-02-05)

Bug Fixes

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)