Changelog

2.8.2 (2024-10-18)

Bug Fixes

Convert pval and qval to heatmap (#123) (478c759)
Move NA values to end of table (#124) (df807a5)
Update max in memory rows for diffexp report (#122) (830e678)

Performance Improvements

Update to latest datavzrd wrapper (#125) (3a4c020)
Update to latest datavzrd wrapper version (#120) (7b2767c)

2.8.1 (2024-09-20)

Performance Improvements

Update datavzrd wrapper version (#118) (e498079)

2.8.0 (2024-09-20)

Features

sort datavzrd tables (#115) (1ccc3fa)

Bug Fixes

Move signed_pi_value columns to the end (again) (#117) (ac4a73b)

2.7.2 (2024-09-11)

Bug Fixes

Fix meta comparison and wildcard issue (#113) (3f8f126)
Fix meta comparison model and label path (#111) (27b9cb1)

2.7.1 (2024-08-22)

Bug Fixes

Move signed_pi_value_* columns into detail mode that dont include the primary variable (#110) (a159b4c)
Move signed_pi_value_* columns to the end and move non primary variable columns to detail mode (#106) (8b2e3fe)
Remove IHW outputs from report (#107) (aa891fa)
Update datavzrd wrapper version (#109) (1fe8c2c)

2.7.0 (2024-08-15)

Features

Improve datavzrd tables (#93) (93512b8)

Bug Fixes

Fix missing output in spia.R when no significant genes are found (#103) (bc0d017)
Handle missing bam columns in units.tsv (#105) (bae88d0)
Remove non-existent outputs in spia rule (#102) (0fbb930)
update to latest datavzrd (417ec3b)

Performance Improvements

datavzrd wrapper v3.12.1, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mb, pure download rules as localrules (#92) (70850fb)
Update datavzrd wrapper (#98) (e5eb0e0)
Update samtools fast separate wrapper (#100) (65d8f41)

2.6.0 (2024-06-05)

Features

Allow bam input files (#94) (4a1f983)

2.5.4 (2024-01-31)

Performance Improvements

improve spia script and report (#83) (4b3cc16)

2.5.3 (2024-01-30)

Bug Fixes

canonical transcript mapped read extraction (#77) (52b56b0)
the above pull request also accumulated a number of other bug fixes and updates:
- QuantSeq data now also works with standard canonical transcripts, when MANE transcripts are not available for a species
- some environment and wrapper updates and fixes, e.g. biomart, pysam, sleuth, datavzrd
- some overall cleanup of the QuantSeq parts of the workflow
- proper QuantSeq testing data, generated with a dedicated workflow and hosted on Zenodo, which enables a quick and useful testing for the respective parts of the workflow

2.5.2 (2023-09-14)

Bug Fixes

simpler three prime QuantSeq cutadapt setup (#78) (ecc9ab7)
update samtools.yaml to latest 1.17 and update github actions (#75) (0fe7948)

Performance Improvements

bump datavzrd wrapper to 2.6.0 and general bug fixes (#80) (657c465)

2.5.1 (2023-06-14)

Bug Fixes

Updated the get-transcript-info.R file and its dependencies (#73) (e44d424)

2.5.0 (2023-05-13)

Features

Support for 3-prime RNA sequencing (#62) (c06c573)

Bug Fixes

fix report labels (#72) (76c7fd9)

2.4.3 (2023-02-06)

Bug Fixes

Feature/update cutadapt wrapper (#67) (29d7967)

2.4.2 (2022-12-02)

Bug Fixes

fix gene-level p-value adjustment (use Benjamini-Hochberg instead of Bonferroni-Holm) (#64) (6ea1682)

2.4.1 (2022-11-04)

Bug Fixes

channel order for bioconductor package download (f57044a)
correct default value for representative_transcripts and check for existence of path (#59) (a85b268)
fix channel order under strict priorities (bdbfb10)
fix default minimum p-value in fgsea (#61) (a6a857d)
for some rules, omit software env when caching (#63) (1d2e3a9)

2.4.0 (2022-03-29)

Features

adapt to fgsea updates, configure fgsea precision by minimum achievable p-value (dcd77ca)