v0.6.0

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)

v0.5.9

0.5.9 (2026-01-07)

Bug Fixes

• Adding Zenodo DOI to Readme (#231) (a3847a9)

v0.5.8

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)

v0.5.7

0.5.7 (2025-10-06)

Bug Fixes

• max 255 read length allowed (#224) (81029df), closes #205

v0.5.6

0.5.6 (2025-10-01)

Features

• bwa additional filtering (#216) (9c81cfd)
• assignment workflow: allow single end reads (FW only) (#218) (9c81cfd)

v0.5.5

0.5.5 (2025-09-17)

Bug Fixes

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

v0.5.4

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)

v0.5.3

0.5.3 (2025-05-13)

Bug Fixes

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

v0.5.2

0.5.2 (2025-05-13)

Bug Fixes

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

v0.5.1

0.5.1 (2025-05-12)

Bug Fixes

• missed config version upgrades (df5391a)