Recent Releases of hmnfusion
hmnfusion - 1.3.0
1.3.0 (2025-04-02)
Features
- bamtofastq, optimize the process and samtools 1.21 compatibility (acaeaaa)
- update snakemake api (7a49c4a)
Bug Fixes
- tests: handling not passing tests (#14) (d02c54f)
- tests: refactor use case (#18) (8a07e7c)
- install_software, skip conda confirmation (56bdbdf)
Styles
- hmnfusion: super-linter (24ce1e8)
- HTML
Published by github-actions[bot] about 1 year ago
hmnfusion - 1.2.0
1.2.0 (2022-06-09)
Features
- commnands: let to output json files for each tool (f114179)
- workflow-align: new docker image to build BAM file, new command to run workflow-align, new command to download reference from zenodo (c185243)
Documentation
Tests
- commands: add json file outputs (8177f1c)
Code Refactoring
- graph: mv tojson(), fromjson() to Graph from extractfusion (04982ea)
- quantification: treatment of argument in commandline (64c51e4)
- utils: excel fmt (5bd759a)
- HTML
Published by github-actions[bot] about 4 years ago
hmnfusion - 1.1.0
1.1.0 (2022-05-06)
Features
- extractfusion: rm input-hmnfusion-bed required (0e7a12f)
- fusion: add mmej atttribute, setmmej(), mmejdataframe() (63ba60a)
- fusion-flag: add command to output all flags (8166d9e)
- fusionflag: add FusionFlag class (a3212ab)
- graph: add subset_graph() (a792f40)
- graph: fix argument type for subset_graph() (a37b271)
- intall-software: add this new feature (63c4825)
- mmej: add mmej_fusion file (7310dfc)
- mmej: add mmej-fusion cmdline (497b013)
- mmej: check fasta index reference (a61956f)
- mmej-deletion: take account multi-sample vcf & refactor to add tests (ad3f510)
- mmej-fusion: add mmej-fusion (0f0082e)
- region: add attributes & functions (1dc4873)
- region: add split_sequence() (c4553a3)
- utils: add bamtofastq() (5f75ef3)
- utils: add base enum str (3d04574)
- utils: add checkfastaindex() (e726873)
- utils: add validatenamesample (d151668)
- workflow: convert bam to fq if needed (fc0c65c)
- workflow: convert bam to fq if needed (17c7180)
Bug Fixes
Styles
- utils: super-linter (db4502b)
- super-linter (a472808)
- super-linter (1e57b48)
- install-software: super-linter (3ac155a)
Code Refactoring
- add debug files properly in local dir (65f589f)
- extractfusion: passing argument name to function (573ee7e)
- graph: rm unused selectnodeinterest() (6f9bd7b)
- mmej: rename to mmej_deletion (7fb0139)
- mmej_fusion: delete unused file (f8df6c7)
- utils: add missing bamtofastq() (c310d9e)
- utils: cmdline(), findexecutable(), bamto_fastq() (2f81f56)
Tests
- fusion: update with mmej attribute (7edc5ee)
- fusionflag: add test for this class (12acb05)
- install-software: add corresponding tests (b929658)
- mmej-deletion: Conclude, Value, MmejDeletion (cf9993e)
- mmej-deletion: super-linter (caac4a0)
- region: update format() (63079fc)
- utils: add bamtofastq(), fq dataset (c0799b2)
- utils: add checkfastaindex() (678f20a)
- utils: bamtofastq (b1e2cf5)
- utils: validatenamesample (70c5580)
- HTML
Published by github-actions[bot] about 4 years ago
hmnfusion - 1.0.0
1.0.0 (2022-03-16)
⚠ BREAKING CHANGES
- command: update command-line
Features
- bed: add hmnfusion bed, defaut in command line & needed for extractfusion (fe02f8f)
- bed: df as argument (239c188)
- commands: check index bam file (a13ed3a)
- docker: add GeneFuse & Lumpy (79dea0b)
- docker: add Lumpy & GeneFuse in Docker image (3a5dda3)
- docker: add several software (b89d22b)
- github: ignore more files (852ab07)
- graph: add to_plot() (63c5473)
- graph: trim node with a bed (379d096)
- utils: add checkbamindex() (d299847)
- utils: add cmdline (38118e7)
- utils: add find_executable() (216f832)
- utils: add validatenamesample() (a5c8e3c)
- worfklow: add snakefile and first commands (0b6684b)
- worfklow: embeded genefuse & lumpy bed (b91dd25)
- workfklow: add fusion-workflow command (ad0863f)
- workflow: add snakefile (23bc591)
- workflow: minor improvments (8ce0975)
Bug Fixes
- bed: rm fip1l1, add pdgfra regions (91a6039)
- docker: add directory to copy lumpy script (1940596)
- docker: put all lumpy files in PATH (0d6aef0)
- graph: take care about cyclic relationship (165f336)
- workflow: hmnfusion, disable threads (97c7f67)
- workflow: misc bugs, adjust env in workflow (4000508)
- workflow: mv Snakefile name (2f04231)
Tests
Documentation
- workfow: add command line example (ca81732)
- update command-line arguments (8d5d985)
- update command-line arguments (37a120d)
- update label entrypoint (c5f7156)
Styles
- workflow: lint black (380d84f)
- workflow: lint black (5e47f14)
- workflow: lint black (410caa3)
- super-linter (2b020c9)
- utils: super-linter (d39eb93)
Code Refactoring
- command: rename command-line (76656e1)
- quantification: update pandas function (42655bf)
- templates: add vcf folder (71a6029)
- test: graph, split consensussingle() & consensusgenefuse_lumpy() (0cc8833)
- workflow: split Snakefile (1640809)
- workflow: use one Snakefile (7ab736a)
- HTML
Published by github-actions[bot] over 4 years ago
hmnfusion - 0.8.0
0.8.0 (2022-02-14)
Features
- github: add test and build actions (982321f)
- add check_region() (b00e2ab)
- add docker image (d675b2f)
- bed, add Bed class (74162c2)
Bug Fixes
- quantification, do not support sam files (960622e)
Documentation
Tests
- add bam dataset (774b287)
- add bed dataset (24c9674)
- add genefuse dataset (7819ff2)
- add hmnfusion dataset (4eaebed)
- add lumpy dataset (c0d9678)
- add software testing (2078fad)
- add test software, extractfusion & quantification (a1d25f1)
- bed, add some tests (7adb9aa)
- ignore dataset lint (d7e3777)
- lint (3c461ec)
- mv dir name (19a85f1)
- mv dir name (e24cb64)
Styles
- black md (23b60f6)
- black style (3ff1388)
- super-linter (da13aa0)
- super-linter (7f4244e)
- super-linter (c5fc45b)
Code Refactoring
- add type & docs (f33665e)
- add typing support (98e9d49)
- linter (38d7ac3)
- linter python isort (fa53dfa)
- mmej, rm unused event argument (5d3a044)
- more generic with dict type (3dade1b)
- mv vcf header from a function to a plain text file (6620fd6)
- region, add check_region as classmethod (6606409)
- respect python isort (96feb70)
- type and doc (a376d71)
- mmej: add type function & docs (c17a073)
- HTML
Published by github-actions[bot] over 4 years ago