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2022-01-12gridss: add somatic variant filteringJustin Bedo
2022-01-05gridss: 2.13.0 -> 2.13.1Justin Bedo
2021-12-06gridss: 2.12.2 -> 2.13.0Justin Bedo
2021-10-29treewide reformatting and simplificationJustin Bedo
- simplify with statix - reformat with nixpkgs-fmt
2021-10-14gridss: 2.12.0 -> 2.12.2Justin Bedo
2021-10-14Revert "gridss: 2.12.0 -> 2.12.1"Justin Bedo
This reverts commit 1ff1c9cf0bcc95a6555d1217598f55b7b9eae866. As per github release page: DO NOT USE: this release has a critical bug in the preprocessing step that removes all split reads
2021-09-21gridss: specify cores for all multithreaded phasesJustin Bedo
2021-09-16gridss: 2.12.0 -> 2.12.1Justin Bedo
2021-08-02gridss: drop softclip to split read conversionJustin Bedo
Unnecessary if aligner supports split reads. Best to leave to user to manage.
2021-05-25gridss: 2.11.1 -> 2.12.0Justin Bedo
2021-04-20gridss: 2.10.2 -> 2.11.1Justin Bedo
2021-02-03add inline documentationJustin Bedo
2020-12-14gridss: 2.10.1 -> 2.10.2Justin Bedo
2020-11-02gridss: 2.10.0 -> 2.10.1Justin Bedo
2020-10-15gridss: 2.9.4 -> 2.10.0Justin Bedo
2020-09-02gridss: shard assembly into 10 pieces by defaultJustin Bedo
2020-07-16gridss: 2.9.1 -> 2.9.4Justin Bedo
2020-05-24gridss: 2.8.3 -> 2.9.1Justin Bedo
2020-04-10gridss 2.7.3 -> 2.8.3Justin Bedo
2019-11-27gridss: 2.7.2 → 2.7.3Justin Bedo
2019-11-20gridss: 2.7.1 → 2.7.2Justin Bedo
2019-11-04gridss: 2.7.0 → 2.7.1Justin Bedo
2019-11-01gridss: 2.6.2 -> 2.7.0Justin Bedo
2019-09-25gridss 2.6.0 → 2.6.2Justin Bedo
2019-09-10gridss: 2.5.2 -> 2.6.0Justin Bedo
2019-08-29gridss: 2.5.1 -> 2.5.2Justin Bedo
2019-08-15gridss: 2.5.0 -> 2.5.1Justin Bedo
2019-07-28gridss: 2.4.0 -> 2.5.0Justin Bedo
2019-06-21gridss: 2.2.2 -> 2.4.0Justin Bedo
2019-04-08grids: add function to include assemblies with annotated VCFJustin Bedo
2019-03-28gridss: 2.0.0 → 2.2.2Justin Bedo
2019-03-06api docs: init GRIDSSJustin Bedo
2019-01-09large refactorJustin Bedo
- use bionix.pkgs instead of nixpkgs - replace stdenv.mkDerivation with stage
2018-12-19gridss: simplify preprocessing and rewrite using new pipe functionJustin Bedo
2018-12-18qsub: refactor overridingJustin Bedo
2018-12-12gridss: refactor identify & annotate variantsJustin Bedo
2018-11-22gridss: restructure gridss pipelineJustin Bedo
2018-11-13Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-11-12Attempt to integrate config file into GRIDSS stagel-d-s
2018-11-07Fix to gridss.l-d-s
2018-10-29Split gridss into constituentsJustin 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.
2018-10-05implement typesJustin Bedo
2018-10-04Refactor to use bionix tree directlyJustin Bedo
2018-09-26Missing GRIDSS filesJustin Bedo
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