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CHANGELOG.md

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Changelog

2.8.2 (2024-10-18)

Bug Fixes

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

2.8.0 (2024-09-20)

Features

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

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

2.5.4 (2024-01-31)

Performance Improvements

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

2.4.3 (2023-02-06)

Bug Fixes

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)