CHANGELOG.md

Changelog

5.7.0 (2024-06-07)

Features

• Add improved visualization for clinical significance (#301) (82eb4dd)
• add linkouts to non-coding tables (#302) (15ce609)
• support selecting the fdr control mode via the config (#306) (ac27206)

Bug Fixes

• download sra (#304) (f77b6be)

5.6.0 (2024-05-04)

Features

• reduce fgbio memory usage (#296) (71611c8)

Bug Fixes

• fusion candidate filtering (#299) (6cc658a)
• use latest datavzrd wrapper that integrates template rendering (#300) (0ad923f)

5.5.0 (2024-04-09)

Features

• add ability to store variants in a population database (BCF) (#288) (e52c29b)
• add alphamissense linkout (#294) (a775627)

5.4.1 (2024-03-28)

Bug Fixes

• use latest wrapper for obtaining known variants (#292) (1268dd9)

5.4.0 (2024-03-23)

Features

• support alphamissense and spliceai (#287) (91a81fa)

Bug Fixes

• update to latest cutadapt (#291) (ca73fa7)
• use latest wrapper for obtaining known variants (#290) (c8cf4df)

5.3.1 (2024-03-12)

Bug Fixes

• avoid piping if there is no glob pattern in the given fastqs (#286) (645e5c0)
• require Snakemake 8 (#284) (9a19971)

5.3.0 (2024-02-27)

Features

• fusion calling (#222) (d0b45ba)

Performance Improvements

• reorganize tests to first only do dry-runs and then run long and short tests in one runner each (#280) (ee973c6)

5.2.0 (2023-11-30)

Features

• colored tick plots in datavzrd report (#279) (757aa0e)
• improve and run sra download ci test case (#276) (074661e)
• map primers by bwa and update datavzrd template (#275) (12f22e9)

Bug Fixes

• unique values when extracting samples column for repeated samples (in multiple groups) (#278) (aaac1b5)

5.1.0 (2023-11-10)

Features

• gene coverage report (#270) (19ee0eb)
• genomenexus link (#271) (16c4a50)

Bug Fixes

• update fastqc wrapper to v1.10.0 to include memory parsing fix (#272) (ed8b391)

5.0.2 (2023-10-09)

Bug Fixes

• remove superfluous import of FTP remote provider (ae68b90)

5.0.1 (2023-08-25)

Bug Fixes

• general fixes and optimizations (#263) (cc486d7)
• sample has umis (#265) (914ddfa)
• switch mem_gb to mem_mb (#262) (6bda9b5)

5.0.0 (2023-08-15)

⚠ BREAKING CHANGES

• make annotations for candidate variant filtering configurable (#251)

Features

• allow umis in both paired end reads (#257) (2fdc798)
• make annotations for candidate variant filtering configurable (#251) (b51bd9d)

Bug Fixes

• allow using one sample in multiple groups (#258) (e336f7a)

4.2.0 (2023-08-10)

Features

• update envs and wrappers (#255) (085df20)

4.1.0 (2023-08-07)

Features

• Handle trimmed fastqs plus additional fixes (#252) (13ae724)

4.0.2 (2023-06-29)

Bug Fixes

• hide binned vaf (#250) (fedd817)
• set id optional (#247) (b91e3a5)

Performance Improvements

• update to varlociraptor 8.3 (#249) (c81c440)

4.0.1 (2023-06-14)

Bug Fixes

• update varlociraptor (#244) (361c9ee)

Performance Improvements

• update to latest datavzrd (#245) (d4ee98a)

4.0.0 (2023-06-12)

⚠ BREAKING CHANGES

• use lowercase for all header names in report tables (#238)

Features

• add binned vaf column for sorting by allele frequency (#240) (a428b30)
• update observation plot to horizontal stacked bars with annotation variable checkbox (#242) (762d3be)
• use lowercase for all header names in report tables (#238) (f142d32)
• use MANE+clinical for selecting representative transcripts (#235) (0af4ba0)

Bug Fixes

• fix mixed up VEP and VEP-cache versions (#241) (86ccece)
• observations plots (#243) (615d9cc)

3.24.3 (2023-05-09)

Bug Fixes

• use annotated calls (#234) (0821a01)

3.24.2 (2023-05-05)

Bug Fixes

• update to latest snpsift, which fixes a bug that before led to loosing some variants (#232) (5586986)

3.24.1 (2023-04-28)

Bug Fixes

• several fixes (#227) (4c5ab31)
• update datavzrd to 2.18.5 (fixes for empty callsets) (#229) (f63479e)

Performance Improvements

• use varlociraptor 8.1 (#228) (e29d9c3)

3.24.0 (2023-04-24)

Features

• Support new varlociraptor 8.0 observations (#225) (925f736)

3.23.1 (2023-04-17)

Bug Fixes

• fix vembrane aux (#223) (245366c)

3.23.0 (2023-04-13)

Features

• handle umis (#213) (61c54e0)
• Improved handling of custom annotation fields (#221) (540f993)

Bug Fixes

• prenthesize combined filter expressions (#214) (fae1b0c)
• update mark_duplicates to newest wrapper syntax (#217) (9d3dd30)

3.22.0 (2023-03-01)

Features

• Add datavzrd fields (#209) (142ead7)

Bug Fixes

• explicitly use categorical type for chi2 testing (#210) (079c756)
• use varlociraptor 6.0 with its new smart FDR control. This leads to improved filtration results with less false negatives (#212) (cb00c33)

3.21.1 (2023-02-17)

Bug Fixes

• fix typo when retrieving candidate filter expression (dd1e661)

3.21.0 (2023-02-17)

Features

• Plot simple observations (#201) (c940ec5)
• Set excluded regions for delly (#203) (3688ea8)

Bug Fixes

• properly handle complex candidate filter expressions including aux files (#205) (6e353f7)

Performance Improvements

• update to varlociraptor 5.10.0 (#207) (076cf4e)
• update to varlociraptor 5.9 (#200) (38135f2)

3.20.1 (2023-02-14)

Bug Fixes

• properly handle missing candidate filter (#199) (bdec1a0)

3.20.0 (2023-02-10)

Features

• add ability to use aux-files for candidate filtering (80f0ba9)

Performance Improvements

• update to varlociraptor 5.8.0 (b15cd85)

3.19.6 (2023-02-01)

Bug Fixes

• provide fasta to vep wrapper, update to latest vep wrapper (814eee3)
• update to latest vep cache wrapper in order to avoid another proxy problem (8f9d1a2)

3.19.5 (2023-01-30)

Bug Fixes

• resource download fixes (proxy support for get_vep_cache, curl deployment for download_revel) (#195) (9e250c6)

3.19.4 (2023-01-23)

Fixes

• update to Varlociraptor 5.6.2

3.19.3 (2023-01-15)

Performance Improvements

• update to varlociraptor 5.6.1 (#189) (4c34c84)

3.19.2 (2023-01-13)

Bug Fixes

• reimplement ability to generate testcase; fix environment for tsv_to_excel rule (#190) (fb2e692)

3.19.1 (2022-12-21)

Bug Fixes

• typo in datavzrd rule (19481c2)
• update to datavzrd 2.11.1 (a98a80f)

3.19.0 (2022-12-13)

Features

• Ordering gene oncoprint rows based on annotation label (#170) (b832e5b)

Bug Fixes

• update to varlociraptor 5.4.1 (#186) (1445902)

3.18.7 (2022-11-24)

Bug Fixes

• fail for empty target regions (#181) (7563aaa)
• Filter offtarget variants (#180) (3c87042)
• remove clinical significance duplicate (#182) (33c28c6)

Performance Improvements

• update datavzrd to 2.9 (#183) (b3e96a2)

3.18.6 (2022-11-15)

Performance Improvements

• update to varlociraptor 5.3.3 (#178) (41fe68a)

3.18.5 (2022-11-14)

Bug Fixes

• fixed output of get_sra rule (#176) (1cfda3a)

3.18.4 (2022-11-11)

Bug Fixes

• Fix empty regions bed file (#171) (feac864)
• omit software env for some rules when checking between workflow cache (#168) (d5899da)

3.18.3 (2022-11-11)

Bug Fixes

• fix revel score download URL (#172) (37bc738)

3.18.2 (2022-10-13)

Bug Fixes

• correctly filter target regions (#166) (29f64fc)

3.18.1 (2022-09-28)

Bug Fixes

• render group labels in oncoprint gene views as heatmaps (6041058)

3.18.0 (2022-09-28)

Features

• update to datavzrd 2.2 (b1c7963)

3.17.1 (2022-09-27)

Bug Fixes

• use latest bcftools concat wrapper which fixes a regression that caused it to just pass on the first given bcf. This was leading to missing a lot of calls! Make sure to rerun with the following: -R merge_calls gather_annotated_calls gather_benchmark_calls bcftools_concat gather_calls if those rules were executed with release 3.16 or 3.17. (56be4e1)

3.17.0 (2022-09-23)

Features

• allow multiple target_regions BED files defined in config.yaml, merging them into one (#161) (84064ef)
• more informative file names (#148) (4b99df9)

3.16.0 (2022-09-01)

Features

• add group annotation capabilities and corresponding display thereof in oncoprint views (#158) (c8aa3f5)

Bug Fixes

• update conda envs and wrappers (if necessary) to work properly with strict priorities (#159) (a5d7be3)

3.15.0 (2022-08-05)

Features

• enhance oncoprint report (#156) (c8357fe)

3.14.1 (2022-07-25)

Bug Fixes

• datavzrd related issues (#152) (dfed4e0)

3.14.0 (2022-05-20)

Features

• Hide columns in datavzrd report (#151) (7db7b35)
• Remove plotdata from datavzrd template (#149) (7d184ff)

Bug Fixes

• automatically calculate genomic sites covered for tumor mutational burden calculation (#130) (7a26dcc)

3.13.1 (2022-05-12)

Bug Fixes

• adjust input (#146) (a70a34b)

3.13.0 (2022-05-11)

Features

• Improve datavzrd tables (#144) (c6ef41c)

Bug Fixes

• update to latest datavzrd, which fixes various little glitches (77b01de)

3.12.0 (2022-05-10)

Features

• render single sample (#140) (2858ca8)

Bug Fixes

• obtain domain for tick plots in datavzrd report from all related columns (#142) (2e57b12)

3.11.0 (2022-05-10)

Features

• use Varlociraptor 5.0 (93568d8)

Bug Fixes

• require Varlociraptor 5.0.3 (22a9b91)
• use latest bwa wrapper to avoid an issue with mamba pulling an old r-base as picard dependency (#141) (c533b27)

3.10.2 (2022-05-02)

Bug Fixes

• defer final output determination to DAG phase (#137) (b551881)

3.10.1 (2022-04-30)

Bug Fixes

• Handle multiple samples (#134) (3a881bf)

3.10.0 (2022-04-26)

Features

• render scenario with yte (#132) (6ba7339)

3.9.0 (2022-04-08)

Features

• use datavzrd for vcf reporting (#115) (631426f)

Bug Fixes

• enable specifying filter-specific vembrane options beyond the filter expression (#121) (5833c45)

3.8.1 (2022-03-23)

Bug Fixes

• make the fasta index an explicit input of rule filter_group_regions (#124) (402a5d9)

3.8.0 (2022-03-12)

Features

• genotyping support, minor fixes, performance improvements and config schema updates, preparation for continuous GIAB benchmarking (#90) (d39b8ac)

Bug Fixes

• ineffective attempt to patch picard syntax usage (#118) (6d66fd6)
• effective fix of picard syntax in configs and in the mark_duplicates rule (#119) (13982fc)

3.7.1 (2022-02-23)

Bug Fixes

• custom-report: Replace indexes of ANN-field by keys (#113) (c355bc1)
• fixed tabix indexing for hg19 REVEL scores

3.7.0 (2022-02-17)

Features

• Plot REVEL-scores (#110) (6fb793c)

Fixes

• refactored primer filtering for having more robust rust script compilation with less external dependencies (#111)