0.6.2 (2026-04-23)
- experiment: 🚑 Do not allow _ or . in Condition or Replicate (b4f3234)
- experiment: 🔥 split_numer was used wrongly when multiple experiments where defined (370411f)
0.6.1 (2026-04-22)
- Assignment: Long read support with pbmm2 mapper (#247) (759453d)
- experiment: 🚀 FWD/REV(/UMI) reads can be splitted into n files before merging (#249) (a41e13e)
- experiment: 🐛 Missing getReads function for correct trimming (440e7bd)
0.6.0 (2026-02-11)
- 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)
- 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)
- correct parameter name in check_version function (7cd50a5)
- snakemake reverted default value handling (#236) (fa5109b)
0.5.9 (2026-01-07)
0.5.8 (2025-10-27)
- 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)
0.5.6 (2025-10-01)
- bwa additional filtering (#216) (9c81cfd)
- assignment workflow: allow single end reads (FW only) (#218) (9c81cfd)
0.5.5 (2025-09-17)
0.5.4 (2025-06-25)
0.5.3 (2025-05-13)
- channel order has to be correct for newer samtools (d0ada2b)
0.5.2 (2025-05-13)
- set htslib and samtools version to 1.21 to avoid ncurses lib clashes (cb59bd4)
0.5.1 (2025-05-12)
- missed config version upgrades (df5391a)
0.5.0 (2025-04-09)
- restructure folders and conda env import. Renaming of rules. Old SLURM ressoucres have to be updated
- IGVF qc metrics report (3ec5012)
- Quality metric json file (for IGVF) and included within QC report (981baac)
- restructure folders and conda env import. Renaming of rules. Old SLURM ressoucres have to be updated (f21cdca)
0.4.7 (2025-04-03)
- 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)
- revert v0.4.5. The fix was already implemented within the common.smk file (7997440)
0.4.5 (2025-02-24)
0.4.4 (2025-02-05)
0.4.3 (2025-01-29)
0.4.2 (2025-01-07)
- swapped barcode output files (a851ad2)
0.4.1 (2025-01-06)
- update configs to 0.4 (bd79b6b)
0.4.0 (2025-01-02)
- Major version change because of changes in config that are not backward compatible.
- 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)
0.3.0 (2024-11-20)
- versioned config (#140)
- 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)
- Support only snakemake >=8.24.1 (#130)
- File output formats and locations changed
- Normalization changed which may result in different outputs
- outlier removal methods (#132)
- No min max length for bbmap. default mapq is 30. (#131)
- IGVF outputs (#129)
- Documentation improvements
0.1.1 (2024-09-30)
0.1.0 (2024-09-18)
First release of MPRAsnakeflow!
- 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
- latest development for new release (#133)
- pseudocounts where not used correctly when RNA or DNA set to 0
- DNA and RNA join correction
- 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)
- 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)