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2021-12-20facets.callCNV: refactor interfaceJustin Bedo
The VCF really is part of config as it's not variants called on the sample but population variants (like dbsnp).
2021-12-14tests: test RG line functionalityJustin Bedo
2021-12-14subread: initJustin Bedo
2021-12-03genmap: initJustin Bedo
2021-10-29treewide reformatting and simplificationJustin Bedo
- simplify with statix - reformat with nixpkgs-fmt
2021-07-28bugfix: use unsorted type for alignment outputJustin Bedo
Most aligners are only pseudo-name sorted (i.e., pairs adjacant).
2021-02-19samtools-index: support cram indexingJustin Bedo
2021-02-03reinstate all testsJustin Bedo
2020-06-27whisper: init 2.0Justin Bedo
2020-02-09lastal: initJustin Bedo
2019-12-18lumpy: initJustin Bedo
2019-12-17Fix shard testJustin Bedo
2019-12-17delly: initJustin Bedo
2019-12-16manta: initJustin Bedo
2019-09-06strelka: default callSomatic to snvsJustin Bedo
2019-09-06test: disable strelka somatic testJustin Bedo
2019-09-06xenomapper: initJustin Bedo
2019-09-06CNVkit: split into multiple outputsJustin Bedo
cnvkit: restructure out to link to multioutputs
2019-08-19snver: require labelled samplesJustin Bedo
SNVer does not extract sample names from the BAM files and labels the columns with the input file paths rather than sample names. We rename the paths to names.
2019-08-16mosdepth: add testJustin Bedo
2019-08-15hisat2: initJustin Bedo
2019-08-15SNVer: init 0.5.3Justin Bedo
2019-07-08tests: add kallisto testJustin Bedo
2019-07-08linkOutputs: refactor output linking expressionJustin Bedo
The existing linkDrv only has a singular output, making it difficult to separate the various types of output. The new functionality replaces the old with attribute sets defining the outputs. The old linkDrv is deprecated.
2019-07-03octopus: initial functionsJustin Bedo
2019-06-21bwa-mem2: initJustin Bedo
2019-06-21Add CNVkit testJustin Bedo
2019-05-09strelka: rewrite to use multiple outputsJustin Bedo
2019-05-09test: enable minimap and snap testsJustin Bedo
2019-05-09fastp: rename run to check for consistency with fastqcJustin Bedo
2019-05-02shard: Implement some basic sharding for FQ filesJustin Bedo
2019-05-02samtools-merge: detect correct sortingJustin Bedo
2019-05-01Add fastp.l-d-s
2019-04-30cleanup examples and stray filesJustin Bedo
2019-04-17snap: initJustin Bedo
2019-04-12minimap2: initJustin Bedo
2019-04-08grids: add function to include assemblies with annotated VCFJustin Bedo
2019-04-07Update example data and expand testsJustin Bedo
2019-01-15strelka: add germline callingJustin Bedo
2019-01-10facets: initJustin Bedo
2019-01-09large refactorJustin Bedo
- use bionix.pkgs instead of nixpkgs - replace stdenv.mkDerivation with stage
2018-12-19link: introduce high-level linking functionsJustin Bedo
2018-12-10bowtie: initJustin Bedo
2018-11-29Revert "test-tnpair: avoid gridss.call while it's broken"l-d-s
This reverts commit 01401aaee74dac39e0502688654ef02771a88cd7.
2018-11-15test-tnpair: avoid gridss.call while it's brokenl-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.
2018-10-25Improve type safety of samtools-mergeJustin Bedo
2018-10-05implement typesJustin Bedo
2018-10-04Refactor referencesJustin Bedo
2018-10-04Add def function to simplify overridesJustin Bedo
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