CHANGELOG.md

Changelog

2.6.0 (2026-04-20)

Features

• paper data (#153) (448a6ea)

2.5.1 (2026-02-16)

Bug Fixes

• fixed and updated version number for ncbi-datasets-cli and unzip (#149) (f4136fb)
• plot isoform performance issue (#152) (4ac1bb7)
• removed 'inputdir' config variable - more flexible, now (#150) (d24e009)

2.5.0 (2025-12-09)

Features

• add ensembl reference download (#135) (8992868)
• add pca (#143) (bd2ceb4)
• adding start and end messages (#139) (1f8fc48)
• enabling caching for reference download rules (#147) (63cee48)
• Implement DESeq2 in R instead of pyDESeq2 (#138) (841cead)
• new cluster profile (#146) (4cdfef0)
• rename transcript ids to gene names (#141) (f3e643f)

Bug Fixes

• changed batch_effect to batch in samples.csv to match config schema (#136) (b20a652)
• profiles dir conformance (#140) (932a899)

2.4.2 (2025-09-10)

Bug Fixes

• dealing with whitespace in transcriptome ids (#133) (582ea7d)

2.4.1 (2025-09-08)

Bug Fixes

• runtime est. for flair diffexp rule (#131) (16f2206)

2.4.0 (2025-09-01)

Features

• add temp marks to intermediary outputs (#128) (c61453c)

2.3.0 (2025-08-01)

Features

• autotomated protein annotation (#115) (3770dff)

2.2.1 (2025-06-12)

Bug Fixes

• resources and config (#117) (508c5bb)

2.2.0 (2025-06-05)

Features

• dynamic resources (#114) (b6db820)

2.1.0 (2025-04-30)

Features

• dynamic resource allocation (#112) (3570e36)

2.0.1 (2025-03-26)

Bug Fixes

• removed subdir from rule to prohibit incorrect wildcard resolution (#108) (e79bebf)

2.0.0 (2025-02-28)

⚠ BREAKING CHANGES

• isoform analysis (#99)

Features

• isoform analysis (#99) (7509cc6)

1.5.0 (2024-11-11)

Features

• local refs (#100) (5fed515)

Bug Fixes

• license from MPL to MIT (#102) (9e987a4)

1.4.1 (2024-10-12)

Bug Fixes

• de correction (#96) (f56f660)

1.4.0 (2024-10-11)

Features

• qm report (#95) (3782c40)

1.3.0 (2024-09-19)

Features

• made output temporary for any files not needed for the report (#92) (a95222b)

Bug Fixes

• taking absolute l2fc values to sort (#91) (9c009d0)

1.2.0 (2024-09-17)

Features

• batch correction (#87) (f174574)
• ci pipeline correction (#90) (c41657a)
• correcting p-values for multiple testing (#66) (a83d514)
• de output (#83) (a2e45bd)
• generate snakemake report (#80) (cd25504)
• get refs from database (#69) (1b50d39)

Bug Fixes

• #82 double p value adjustment (#84) (1d6bfc7)
• batch correction (#89) (04fcfcf)
• different names for downloads to avoid name clashes (#71) (756ba5b)
• quantification (#74) (3d9216e)
• quantification input output mismatch (#68) (44e6451)

1.1.0 (2024-08-16)

Features

• added new config files for cluster specific configurations (#48) (966e059)
• added wrappers (#46) (9c3bfe4)
• env update (#45) (030e041)
• map qc (#38) (4d5b8bc)
• qc rules (#16) (3237e2c)
• read length filter (#44) (10a8d93)
• Rules moved from snakefile to corresponding SMK files in rule folder. (#54) (ee3dfc1)

Bug Fixes

• added import sys for log (#36) (0f8ac63)
• added new samples to config (#39) (b993b01)
• deployment (#64) (5b137c3)
• env update (#42) (704b25c)
• fixed read filter.py for read_length=0 (#50) (992346b)
• linting for github actions (#56) (54605ae)
• lookup #18 (#19) (ed226a3)
• pydeseq2 (#52) (f8d566a)
• read quantification (#22) (71422a1)
• write de params (#62) (b4fb2be)

1.0.0 (2024-04-30)

Features

• added dummy 2nd contition to sample file (812fc8a)
• customization: mostly scriptizing for snakemake (354a91c)

Bug Fixes

• env: fixed env for slurm and fs plugins (65862e0)
• param: updated profile for human readable times (a0395a2)
• removed 'resdir' parameter from config file (b28fdfe)
• using configurable 'MAMBA_EXE' env var instead of a specific conda command (a4b6e18)