bionix.git - Functional, highly-reproducible bioinformatics pipelines

Age	Commit message (Collapse)	Author
2022-02-09	don't strip store paths from bams	Justin Bedo
	Due to BAM compression attempting to strip store paths is a waste of time.
2021-10-29	treewide reformatting and simplification	Justin Bedo
	- simplify with statix - reformat with nixpkgs-fmt
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

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

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

2018-11-22	gridss: fix configure file optional string error	Justin Bedo

2018-11-15	gridss.softClipsToSplitReads: sort ordering is not preserved	Justin Bedo
	NB: this breaks gridss.preprocessBam
2018-11-13	Merge branch 'master' of https://github.com/PapenfussLab/bionix	l-d-s

2018-11-12	Attempt to integrate config file into GRIDSS stage	l-d-s

2018-11-07	Add bwa to softClipsToSplitReads	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.