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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
2019-06-18slurm: fix bug with srunJustin Bedo
salloc must call srun to actually launch job on execution node rather than submission node
2019-06-14slurm,qsub: update to allow chaining of execution enginesJustin Bedo
Previously exec was redefined to defer to slurm/pbs for execution. This did not chain the previous exec, meaning you couldn't chain execs.
2019-06-11qsub: parameterise the path to PBS utilsJustin Bedo
2019-06-11slurm: allow salloc path to be overridden in stage callsJustin Bedo
salloc was missing from defaults, preventing overriding of salloc path for each stage.
2019-06-06Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2019-06-04strip: handle non-buildCommand based stagesJustin Bedo
2019-05-22Unested picard-markDuplicates.l-d-s
2019-05-16slurm: renamed from sbatchJustin Bedo
2019-05-16stage: fix multicore tagging to work with derivation overridingJustin Bedo
2019-05-14strip: remove store paths from outputs to minimise closuresJustin Bedo
2019-05-02shard-regex: split into separate file to fix exec issuesJustin Bedo
2019-05-02shard: Implement some basic sharding for FQ filesJustin Bedo
2019-05-01Add fastp.l-d-s
2019-04-18sbatch: initial slurm implementationJustin Bedo
2019-04-17snap: initJustin Bedo
2019-04-12minimap2: initJustin Bedo
2019-04-07update stage names to include bionix- prefixJustin Bedo
2019-03-15add multicore passthru flagJustin Bedo
2019-03-01ascat: initJustin Bedo
2019-02-06qsub: rename flags to qsubFlags to avoid collisionJustin Bedo
2019-02-06qsub: parameterise queue and allow arbitrary flags to be passedJustin Bedo
2019-01-23stage: change to stdenvNoCCJustin Bedo
2019-01-10facets: initJustin Bedo
2019-01-10cnvkit: initJustin Bedo
2019-01-09large refactorJustin Bedo
- use bionix.pkgs instead of nixpkgs - replace stdenv.mkDerivation with stage
2019-01-09split/join/each: introduce functions for splitting/joining drvsJustin Bedo
2019-01-08snpeff: initJustin Bedo
2018-12-19bionix: export nixpkgs.lib as bionix.libJustin Bedo
2018-12-19link: introduce high-level linking functionsJustin Bedo
2018-12-18pipe: fix bugJustin Bedo
2018-12-18pipe: reverse function compositionJustin Bedo
2018-12-18qsub: refactor overridingJustin Bedo
2018-12-10bowtie: initJustin Bedo
2018-11-20Add some typed fetchurl functionsJustin Bedo
2018-11-02kallisto: initJustin Bedo
2018-10-26init: mutectJustin Bedo
2018-10-23Wrap inferCNVJustin Bedo
Resolves #8
2018-10-05implement typesJustin Bedo
2018-10-04Add defQsub functionJustin Bedo
2018-10-04Add def function to simplify overridesJustin Bedo
2018-10-04Add qsub function to override all attributesJustin Bedo
2018-10-04Refactor to use bionix tree directlyJustin Bedo
2018-10-03refactor reference location to libJustin Bedo
2018-09-28Add crumbleJustin Bedo
2018-09-26Add GRIDSSJustin Bedo
2018-09-26Add qsub to bionix top levelJustin Bedo
2018-09-26Add flagstat and fastqcJustin Bedo
2018-09-26refactor, add mosdepth, and fixes for bwaJustin Bedo
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