Changelog

5.8.0 (2025-02-12)

Features

Bug Fixes

  • remove nanosim TODO by using new pre-trained models and latest version of nanosim in the wrapper (#3648) (01c4cb4)

Performance Improvements

5.7.0 (2025-02-07)

Features

Performance Improvements

5.6.1 (2025-02-04)

Performance Improvements

5.6.0 (2025-02-03)

Features

  • add expected output checking to test_wrapper.py run() function (fix: ensembl-reference wrapper download >1 chromosome) (#3432) (53cfae1)

  • Add support for seqkit split2 (#3575) (7250679)

  • allow snakemake object access in datavzrd config template (#3598) (0018aa9)

  • Deeptools bampefragmentsize (#3596) (6e90858)

  • Varscan2 - SnpEff Meta wrapper (#3501) (71a8434)

Performance Improvements

5.5.2 (2025-01-17)

Performance Improvements

5.5.1 (2025-01-10)

Performance Improvements

5.5.0 (2024-12-10)

Features

Performance Improvements

  • Update datavzrd wrapper to latest yte version (#3537) (336079b)

5.4.0 (2024-12-06)

Features

Performance Improvements

5.3.0 (2024-11-27)

Features

5.2.1 (2024-11-22)

Performance Improvements

5.2.0 (2024-11-21)

Features

Performance Improvements

5.1.0 (2024-11-14)

Features

5.0.2 (2024-11-11)

Bug Fixes

  • in seqkit wrapper, allow multiple inputs for stats (#3430) (65ed4ed)

Performance Improvements

5.0.1 (2024-11-05)

Bug Fixes

  • fixed datavzrd environment pinning to include numpy, pandas and polars (#3426) (5d3b18b)

5.0.0 (2024-11-01)

⚠ BREAKING CHANGES

  • better names for quast wrapper output files (#3377)

Bug Fixes

  • better names for quast wrapper output files (#3377) (6573e25)

Performance Improvements

4.8.0 (2024-10-31)

Features

  • create nanosim wrapper for all three modes of simulator.py (#3165) (d533df5)

4.7.8 (2024-10-31)

Bug Fixes

  • add support for ht2l indexes in hisat wrapper (#3371) (b373a33)

  • allow for arbitrary output files in quast wrapper (#3373) (aff7c02)

  • issue when input files are in subfolders in merqury wrapper (#3372) (9b354fc)

4.7.7 (2024-10-31)

Bug Fixes

  • Add additional dependencies to Datavzrd wrapper (#3374) (fa4e13f)

  • gffread issue with reading gff files, writing fasta files (#3367) (e72fca0)

4.7.6 (2024-10-25)

Performance Improvements

4.7.5 (2024-10-23)

Performance Improvements

4.7.4 (2024-10-23)

Performance Improvements

4.7.3 (2024-10-23)

Bug Fixes

4.7.2 (2024-10-16)

Bug Fixes

Performance Improvements

4.7.1 (2024-10-09)

Performance Improvements

4.7.0 (2024-10-04)

Features

Bug Fixes

  • Gatk filter mutect call typo (#3295) (6295e37)

  • Gatk learn orientation model with multiple input files (#3296) (250dd3e)

Performance Improvements

4.6.0 (2024-09-25)

Features

Performance Improvements

4.5.0 (2024-09-20)

Features

Bug Fixes

Performance Improvements

4.4.0 (2024-09-17)

Features

  • adds GRCm39 to default_effective_genome_size in deepTools bamCoverage (#3164) (b5916c4)

  • Bwameth index (#3162) (bb4acf9)

Performance Improvements

4.3.0 (2024-08-28)

Features

4.2.0 (2024-08-23)

Features

Performance Improvements

4.1.1 (2024-08-21)

Bug Fixes

4.1.0 (2024-08-21)

Features

  • Allow outputting of rendered yte config in Datavzrd wrapper (#3123) (e74be78)

Bug Fixes

  • Correctly handle non str index list for bwa-mem2/mem (#3101) (6f46508)

Performance Improvements

4.0.0 (2024-08-14)

⚠ BREAKING CHANGES

  • switch to nonpareil utils script for plotting (#3100)

Features

3.14.2 (2024-08-13)

Performance Improvements

3.14.1 (2024-08-09)

Bug Fixes

Performance Improvements

3.14.0 (2024-07-31)

Features

  • add new wrapper to create annotation tables via Ensembl biomart (#3072) (07dc088)

Performance Improvements

3.13.8 (2024-07-18)

Performance Improvements

3.13.7 (2024-07-12)

Bug Fixes

Performance Improvements

3.13.6 (2024-07-08)

Performance Improvements

3.13.5 (2024-07-05)

Bug Fixes

  • change from wget -o (log file output) to -O (proper output file output) (#3059) (a0e5045)

Performance Improvements

3.13.4 (2024-07-03)

Performance Improvements

3.13.3 (2024-06-28)

Performance Improvements

3.13.2 (2024-06-27)

Performance Improvements

3.13.1 (2024-06-26)

Bug Fixes

Performance Improvements

3.13.0 (2024-06-24)

Features

  • add new ensembl-regulation wrapper to systematically download Ensembl regulatory_features (#3017) (a81ced2)

3.12.2 (2024-06-24)

Performance Improvements

3.12.1 (2024-06-12)

Performance Improvements

3.12.0 (2024-06-07)

Features

  • Support lists in param.region, and fix typo (#2978) (1e9e511)

Performance Improvements

3.11.0 (2024-05-31)

Features

Bug Fixes

Performance Improvements

3.10.2 (2024-05-03)

Performance Improvements

3.10.1 (2024-05-02)

Bug Fixes

  • allow input access in config rendering for datavzrd (#2917) (167ed76)

3.10.0 (2024-05-02)

Features

  • Add wrapper for filtering TTree in ROOT (#2900) (c294552)

  • enable YTE templating in datavzrd config file (#2916) (97262a5)

Performance Improvements

3.9.0 (2024-04-22)

Features

Bug Fixes

Performance Improvements