hydra-genetics v0.2.2

Bug Fixes

• juli_filter: correct parameter name (2a2f2c7)

hydra-genetics v0.2.1

Bug Fixes

• filter_juli: corrected scripts path (70a8cfc)

hydra-genetics v0.2.0

Features

• added DNA fusion caller JuLI rules (06aa8c7)
• added fusion filtering (db7aca7)
• remove time consuming default setting in fusioncatcher (06c3475)

Bug Fixes

• correct common container (7ee6059)
• juli_call: command bugfix (d83faf5)

Documentation

• corrected path to hydra-genetics logo (fc940a0)
• JuLI: added documentation (36f5005)

hydra-genetics v0.1.0

Features

• Add arriba fusion caller (2526e06)
• add compatibility test (1741fef)
• added extra parameter (ddd72fe)
• added fuseq_wes and filtering (3362090)
• added rule for drawing Arriba fusions (d0267bd)
• added star-fusion (f8ee474)
• added threads (d4e8476)
• ci: add workflow for semantic commits (a654493)
• ci: pull-request template (a80ddc3)
• drop conda support and testing (676db90)
• filter fuseq_wes based on file with fp fusions (c1d9693)
• fusioncatcher (df02e7b)
• make config.yaml location more flexible (8cef602)
• make configfile/confgilefiles argument mandatory (49f6ddb)
• new arriba version (35ed724)
• New rule: gene_fuse for DNA-fusions (0405e74)
• Rule for reporting only true fusions (hardfilter) (15582e9)
• Rule for reporting only true fusions (hardfilter) (69a20d2)
• update snakemake version, allow range up to version 8 (1872c52)
• update snakemake-version (51d2ce9)
• update snakemake-version (73c8593)

Bug Fixes

• add missing file used by readthedocs (ad33a78)
• added .bai file as input to arriba_draw_fusion (14639e1)
• bugfix same fastq for both mates (1a0445a)
• change run column name to flowcell in units. (1cfaf7f)
• container: added env file for fusioncatcher (b0826cf)
• extra param (f21180d)
• extra parameter (4f1e30a)
• fake directory for starfusion dry run (777e3d3)
• fix path to script (1b0e67c)
• get on input files (8daaf50)
• input dir for R (b3b71b4)
• input dir for R (b53f788)
• log and benchmark files (aa22e04)
• make sure that snakemake doesn't remove all output folders (b3b71b4)
• make sure that snakemake doesn't remove all output folders (9c64d4e)
• missing comma (864fb97)
• new config for star_fusion (23bddf2)
• output dir for R (d5c1375)
• output file names (7e5eb5a)
• output file names (1ba8d48)
• output to file adapted to dicts (f627281)
• remove output files (f852a2b)
• remove priority (7433b54)
• removed unnecessary install of mamba (d10d913)
• reposition parantheses to include all flags (4ef06c4)
• set {} as default for config.get (43fe26e)
• update mkdocs rule plugin version to handle comments in rule (489ef35)
• update mkdocs_rule_plugin to handle comments (dc17a18)
• updated requirements (d73d20c)
• working docker (1d65f97)

Documentation

• added all rtd for all remaining rules (571f9e1)
• added rts up until fuseq_wes (ac15d6d)
• update mkdocs rule plugin (ef6b075)
• update pycodestyle link (0a7458f)
• updated README (302d365)