Releases: hydra-genetics/cnv_sv
Releases · hydra-genetics/cnv_sv
hydra-genetics v0.7.1
hydra-genetics v0.7.0
hydra-genetics v0.6.0
Features
- add chr to chromosome if missing (0197bb2)
- add sniffles2 single sample calling (0ce9b8a)
- add tabix and bgzip for vcf output (f29e4a2)
- add trgt (145641d)
- added cnvkit call of jumble output (605ce90)
- added jumble_vcf rule for segment exports (0aa2632)
- added the CNV caller Jumble (4d24aa8)
Bug Fixes
- add default values for pacbio_alignment and ont_alignment in config.schema.yaml (ddedade)
- change to compatible wrapper (4759cff)
- code improvement (911422a)
- common: set type to str for pandas dataframe (4c0e0f2)
- correct input parameter name (1722db4)
- corrected output file names (238fb36)
- jumble_vcf should have same parameters as cnvkit_vcf (1748415)
- make sure sample column is a string (2d3aa6b)
- missing parenthesis (be912f8)
- update common container (409dbda)
- Update config_pacbio.yaml (e7f6117)
- Update config.yaml (c2a82f8)
- Update config.yaml (ea9a0f7)
- Update config.yaml (794e3d6)
- wrong config parameter name (3ad5336)
Documentation
hydra-genetics v0.5.0
Features
- add names for the vcfs using params and add bnd_distance param (e32ca47)
- add priority as a param (db6e1ba)
- make the tumor cell content optional (#160) (1c960c6)
Bug Fixes
- add missing space in command (21e2767)
- add quite to picard for stdout (8f09906)
- added RTD for all reviewer rules and fix rule name (3a81357)
- allow missing TC when generating GATK VCF (#162) (aa6fece)
- bump snakemake version to support apptainer (#151) (eb4b05d)
- cnvpytor: add bam index as input (60c840a)
- handle that cns files can have different number of columns (57da77b)
- incorrect type for copy number thresholds (#164) (b549266)
- pin pulp version to <2.8.0 (1c960c6)
- rm extra } in benchmark name (e2f34ce)
- specify model when calling and filtering in cnvpytor, and threads in readdpth rule (4347806)
- svdb: use the overlap and extra params (fe656a9)
- update container for rule pindel_update_vcf (#161) (512a924)
Performance Improvements
- add bcftools reheader to pindel vcf for correct samplename (fcadaba)
Documentation
- added RTD files and the rules for automap and cnvkit (ce2f2ca)
- added RTD for all manta rules (2571744)
- added RTD for all pindel rules (b0ca4da)
- added RTD for all purecn rules (7211b29)
- added RTD for all smncaller rules (ed55b6b)
- added RTD for all svdb rules (1cdd6ba)
- added RTD for cnvpytor and exomedepth (8fd490a)
- added RTD for expansionhunter (4f290ca)
- added RTD for gatk cnv rules (a0a575e)
- added RTD for tiddit rules (fea5964)
- added RTD for upd rules (2eccfe5)
- dag graph (7a654c2)
- organise rules based on software (36568d9)
- Update docs/softwares.md (d3e3f67)
- Update docs/softwares.md (188ef59)
- Update docs/softwares.md (90ad983)
- Update docs/softwares.md (dd02db5)
- Update docs/softwares.md (6f16c13)
- Update docs/softwares.md (25b3195)
- Update docs/softwares.md (c02990c)
- update to new rule plugin (aedbdfd)
- Update workflow/schemas/resources.schema.yaml (6136f71)
hydra-genetics v0.4.1
Bug Fixes
- change to config.get in exomedepth_call (34f5753)
hydra-genetics v0.4.0
Features
- add upd (cc5a660)
- exomedepth: add checkpoint rule to allow reference file as input (a75d1e5)
- exomedepth: Add option to run exomedepth with hg38 (179bab3)
- remove conda support and testing (0a3610d)
Bug Fixes
- automap input and integration test (20ec062)
- exomedepth: chosse female ref when the peddy sex is NA (4357702)
- get output (fb11ed2)
- get samples filename from config, close #135 (46b53c6)
- linting (e28d277)
- out_dir (55a13f0)
- output (8b8af48)
- tests for sutomap (33a384e)
- tsv to pdf (3aa56c7)
- typo (d5cb0ca)
Documentation
hydra-genetics v0.3.1
hydra-genetics v0.3.0
Features
- added default in function (bf4f3f2)
- added function that extracts purity for purecn (9cf298e)
- added pathology option (4b3adc5)
- added rule purecn_purity_file (2bed973)
- added tags for purity method (b9f3d3d)
- svdb is now configurable to tc method (c3eb2e1)
Bug Fixes
- added backslash in cmd (994fa78)
- allow purecn to run on all sample types (6947acf)
- bugfx (ff30237)
- corrected get_tc function output (3c89633)
- input file now with germline annotation (bb7e5dd)
- output files (97fb714)
- rename caller from gatk_cnv to gatk (6c0d00f)
- rule name and output folder (003f415)
- tc files only in params and does not trigger purecn (28bdbe4)
Documentation
hydra-genetics v0.2.0
Features
- Initial PureCN implementation (827ecd5)
- run expansionhunter with sex from peddy (96248bf)
- update pindel call wrapper (deca8ee)
Bug Fixes
- Add cnvkit_seg output (6b2bc02)
- Add dummy intervals file for dry-run (c36efa8)
- Add mutect2 VCFs for PureCN (58c4784)
- Add required parameters for purecn (a6771a6)
- fix integration test problem (139c948)
- fun_segmentation is a required property for purecn (2376c99)
- make run step of manta require bam as input to prevent bam files from being cleaned away (5918c73)
- Minor language tweaks (aebacab)
- Re-order resources in rules (1c889d4)
- Rename cnvkit_seg log and benchmark (c9f2808)
- Resolve snakefmt warnings (fa7651e)
- Resolve snakefmt warnings (b738559)
- Separate PureCN output rule (ef80f60)
- Simplify expected PureCN output (22fb008)
- tiddit: fix env and bam to work with tiddit (6803a15)
- Typos in output definitions (106edaa)
- Use dummy intervals (8bcdae0)
- Use hydragenetics container for cnvkit_seg (65bd30b)
- Use same conda env for all PureCN rules (a795870)
Documentation
- README: change header to regular text (d0e74d4)
hydra-genetics v0.1.0
Features
- Add 3 rules for pindel plus envs and script (5c51855)
- add conventional-prs workflow (94cc587)
- add exomedepth (ebfe037)
- Add logging and make script testable (167a148)
- add missing entry in schema (61a7055)
- Add rule cnvkit_call_loh which adapt calls according to TC (3837d51)
- Add rule to generate cnvkit diagram (bef8828)
- added bedfile to pindel call (36aca30)
- Added environments (c919fed)
- Added manta rules (e77071d)
- Added rule cnvkit coverage (7162e00)
- Added rule cnvkit_call together with test files (4d7c808)
- Added rule cnvkit_create_access (7d5a550)
- Added rule cnvkit_create_antitargets (5fd5d12)
- Added rule cnvkit_create_targets (cdb3f5e)
- Added rule for manta tumor only calling. Refactor of old rule (530a295)
- Added rule GATK_cnv_collectAllelicCounts (d4abf5e)
- Added rule GATK_cnv_collectReadCounts (66ab8f7)
- Added rule GATK_cnv_denoiseReadCounts (99822b5)
- Added rule GATK_cnv_modelSegments (8c88d06)
- Added rule germline_vcf (9bbabc4)
- Changed cnvkit_vcf to own script (db9a85d)
- Generate output list programmatically (ef95803)
- germline vcf now performed by filter vcf using pipeline config and override in Snakemake (0a427b6)
- make config.yaml location more flexible (f6f4416)
- make configfile/confgilefiles argument mandatory (02b4f25)
- make module compatible with latest version of snv_indels and alignment module. (8ea6383)
- make output more configurable (dbd9bbf)
- Make unnecessary manta output vcfs temp (46688c2)
- manta: added extra params to manta (e99460f)
- new rule cnvkit_vcf that exports segment files to vcf (9769357)
- New rule svdb (e7349b4)
- Prepare pindel config script for unit testing (13b0264)
- setup integration test for exomedepth (7a30fc0)
- update snakemake-version (830124c)
- update svdb version (d6745f6)
- Upgrade pindel to wrapper v85.0.1 (9048434)
Bug Fixes
- add containers and change from bcftools view to zcat in rule germinline_vcf (5fa941f)
- add contigs to pindel-vcf (4a52b00)
- add library to install for exomedepth (63d19c2)
- Added resources, rule name fix, rm testfiles, rm wp1 in config (f408a14)
- better vcf annotation for filtering (8aa6da8)
- bugfix (140842c)
- change run column name to flowcell in units. (a69af37)
- change TC to tumor_content (8c11ee6)
- change to point to master (41e6d16)
- change type from float to number (1731573)
- Changed name again (ea530f1)
- cnvkit: change python version (f315187)
- cnvkit: change to correct conda env file (be3d3ba)
- Correct runWorkflow script path and add container to config (057b151)
- don't install snakemake using mamba (dc08143)
- float in header (4e30d39)
- float in header (7c0c233)
- handling of multiple databases (978d218)
- info ids to long (541bd8d)
- int to float in vcf headers (331da1d)
- lock singularity version to prevent bug with latest version (bfe978e)
- reference under rule (92fd035)
- remove unused dependency. (81f7ed6)
- revert changes (e74b497)
- rule name change (f617b06)
- set correct env file (c81d30d)
- set strict mode for conda (d070bda)
- update r script to handle empty results (6bd463b)
- used corrected cn instead of cn (dc59207)