hydra-genetics v1.1.0

Features

• Add option to merge af for complex variants (b8129c3)
• New rule to handle af from complex variants (b881c57)

Bug Fixes

• Added noqa-tag on import to pass pycodestyle (b88b397)
• Fixed snakefmt linting error (e9ae6b8)
• Handling of invalid input parameter (223785c)
• KeyError handling and additional unittest (1604d9c)
• pycodestyle-fix (9a5cee6)
• Removed deprecated Mambaforge added Miniforge (629e1b5)
• Removed non used format- and info-keys (3186f38)
• Rulegraph as png (a7e6b48)
• Update config/config.yaml (1c2cacf)
• Update to Miniforge3 (b21d8f1)
• Updated rulegraph with merge_af_complex_var. (2419bff)
• Use apptainer instead of singularity (fcfa01f)

hydra-genetics v1.0.0

⚠ BREAKING CHANGES

• constrain bgzip and tabix to only work within module

Features

• add intermediate results directory (fe5226f)
• added ruleorders (be2d4f6)
• constrain bgzip and tabix to only work within module (e37c9ed)
• use the run_deepvariant script (1465ad0)

Bug Fixes

• pulp (6c11be8)
• remove extra pulp in requirements (82477de)
• tabix: fix log filename (a64e1fd)

Documentation

• add deepvariant to softwares.md (87988a0)
• explain the optional gVCF output for deepvariant (de20ce7)
• update mkdocs snakemake plugin (298983b)

hydra-genetics v0.6.0

Features

• fix_af: add deepvariant (08489b8)

Bug Fixes

• sort shouldn't require a tbi file (bee2ec0)
• update schema with correct key value for gatk_mutect2_filter (1f147fb)

Documentation

• add file used to build docs at readthedocs (0710507)
• added all remaining rules (4992b47)
• added description of rule graph generation (f077c95)
• added documentation for rules up to gatk (bb81083)
• added rule graph (c5b04bb)
• fix table in intro.md (1d62e06)
• include bugfixed rule (1199c11)
• update docs (f2da493)
• update mkdocs plugin version (decd144)
• update plugin version (8c2eee8)
• update plugin version (ae5291c)
• update simplified rulegraph for readthedocs (3e1d751)

hydra-genetics v0.5.0

Features

• update snakemake version, allow range up to version 8 (fdb57fe)

Bug Fixes

• deeptrio: specify bam index files in the input for make examples (eddf9f5)

hydra-genetics v0.4.0

Features

• Add deeptrio (6fa6952)
• add deepvariant (ca464cf)
• make gatk_pass_filter configurable (7f65825)
• remove conda env/testing (bc72d83)

Bug Fixes

• fix_af.py (cd0a0d2)
• update config (9145272)
• Update workflow/schemas/config.schema.yaml (4a6a939)

Documentation

• update CODEOWNERS (d7f8fa1)

hydra-genetics v0.3.0

Features

• make config.yaml location more flexible (d0a5296)
• make configfile/confgilefiles argument mandatory (a860631)
• update snakemake-version (3d5ed33)

Bug Fixes

• added multiallelic variants to mutect2_pass_filter (94d1a42)
• make sure tabulate version is under 0.9.0 (9bb1fbe)
• set strict mode for conda (47a7581)

Documentation

• update compatibility (00805a9)
• update readme information (fffecea)

hydra-genetics v0.2.0

Features

• added mutect2 filtering rule (6a831f2)
• added mutect2 filtering schemas (0e09f6d)
• added rule for hard filtering of mutect2 (983f889)
• update wrapper version (669460f)

Bug Fixes

• adapted tests after new rulenames (6f51241)
• added temp on output (1b9c950)
• bugfixes (25ad129)
• bugfixes and testing (fd71a2c)
• correct singularity (2867d9d)
• update compatibility config-file (79d76e6)
• update config, mutect2 to gatk_mutect2 (883b579)
• update path, mutect2_gvcf to gatk_mutect2_gvcf (111cd4e)
• wrong parameter name (3630413)

Documentation

• new rulegraph and updated readme (58bcf0d)
• update compatibility list (53cf137)

hydra-genetics v0.1.1

Documentation

• update README to include haplotypecaller (14e1367)

hydra-genetics v0.1.0

Features

• add compatibility test against alignment module." (7237bf0)
• add conventional-prs workflow (ceba918)
• Add logging, refactor and fix some bugs (8c5c09f)
• add pull-request template (14250d1)
• add resources to rules. (d1a0efd)
• Add tabix indexing rule. Also adapted merg_vcf to take indexed vcf as input. (a27cb03)
• added annotate rule (601c698)
• Added decompose, normalize and sort of vcf files (69a14b7)
• added release-please workflow (8e171e1)
• Added rule ensemble_vcf (bcbio recall). Also made sort_vcf more general. (4d6464c)
• Match rules to standard, optimize, add functions (c3185f9)
• moved rule: filter_vcf_on_format move to filtering module (ebd1f41)
• moved rule: filter_vcf_on_format move to filtering module (3e3207e)
• mutect2 rule (202e7c2)
• new rule bed_split. Changed reference and bam files (cf9dcd7)
• New rule bgzip for vcf-files (3ab1abd)
• New rule merge vcf (0f275ba)
• New rule mutect2_gvcf that generates a gvcf instead of vcf (0e1abcc)
• New rule: fixAF (bdd4efd)
• New rule: merge_gvcf (cf250cd)
• New vardict rule (517129f)
• Remove snver, fix error message (0ed6b16)
• Rule for filtering of vcf files. Also added env for conda. (1566924)
• update version of common container (52b7b6b)
• Use barcode as part of units index and set wildcard constr (d52c2cd)
• Use g.vcf extension for gvcf files (eacc3a3)

Bug Fixes

• Added bam-index as input to vardict (4c6d72b)
• change run column name to flowcell in units. (5385f22)
• Downgrade conda package versions to avoid crash (061365a)
• fixed bam location based on alignment prep-release (d08edb3)
• lock singularity to version that works with our images from dockerhub (5115f39)
• Vardict skips reads with mapq 0. Also, correct columns in bed file as default (72be218)

Documentation

• Add latest rule graph (037d108)
• update pull-request template (79f7cfb)
• Update README (4a237f0)