bionix.git - Functional, highly-reproducible bioinformatics pipelines

Age	Commit message (Collapse)	Author
2021-10-29	treewide reformatting and simplification	Justin Bedo
	- simplify with statix - reformat with nixpkgs-fmt
2021-07-28	bugfix: use unsorted type for alignment output	Justin Bedo
	Most aligners are only pseudo-name sorted (i.e., pairs adjacant).
2020-11-30	gridss.assemble: fix workdir manipulation	Justin Bedo

2020-09-02	gridss: shard assembly into 10 pieces by default	Justin Bedo

2020-09-02	gridss: add missing flags parameter	Justin Bedo

2019-03-28	gridss: less chatty logs	Justin Bedo

2019-03-15	add multicore passthru flag	Justin Bedo

2019-01-09	large refactor	Justin Bedo
	- use bionix.pkgs instead of nixpkgs - replace stdenv.mkDerivation with stage
2018-12-11	Merge branch 'master' of https://github.com/PapenfussLab/bionix	l-d-s

2018-12-11	gridss: fix softClipsToSplitReads after assembly	Justin Bedo

2018-12-10	gridss: add java heapSize arguments.	l-d-s

2018-12-10	gridss: fix tmpdir bug.	l-d-s

2018-11-29	Correct argument for gridss option file	l-d-s

2018-11-29	gridss: fix for nix installations outside of /nix	Justin Bedo

2018-11-26	Also need config for 'assemble' step.	l-d-s

2018-11-22	Merge branch 'master' of https://github.com/PapenfussLab/bionix	l-d-s

2018-11-22	gridss: restructure gridss pipeline	Justin Bedo

2018-11-15	Fix up gridss config file.	l-d-s

2018-11-15	Need to test config != null	l-d-s

2018-10-29	Split gridss into constituents	Justin Bedo
	Wrap each individual command for GRIDSS so that bionix executed the pipeline rather than GRIDSS. This patch introduces a "call" function that executed the whole pipeline in bionix on an arbitrary BAM file. Resolves #10.