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2022-01-06strip: rollback simplificationJustin Bedo
Fails sometimes when output is not a directory. This patch reverts to the previous implementation, but also patches in a fix for file names containing spaces.
2022-01-05fix bug in strip-store-pathsJustin Bedo
also taking the opportunity to simplify the rewriteOutput function and handle filenames with spaces
2021-12-20rewrite strip store pathsJustin Bedo
Old version used sed, which is not inplace and causes issues when garbage collection triggers during a build. This patch adds a small rewriter that works in place.
2021-12-14subread: initJustin Bedo
2021-12-06parameterise RG line as nix attribute setJustin Bedo
Allows more seamless transitioning between alingment algorithms
2021-12-03genmap: initJustin Bedo
2021-10-29treewide reformatting and simplificationJustin Bedo
- simplify with statix - reformat with nixpkgs-fmt
2021-06-25linkOutputs: passthrough the inputs to make it easier for downstream ↵Justin Bedo
expressions to refer to build products
2021-02-08refactor slurm implementation to allow for overlaysJustin Bedo
2021-02-08don't recursive update overlaysJustin Bedo
2020-11-17implement overlaysJustin Bedo
2020-11-16sambamba: initJustin Bedo
2020-11-02star: initJustin Bedo
2020-06-27whisper: init 2.0Justin Bedo
2020-04-22fix error message for linkOutputsJustin Bedo
2020-03-27pipe now part of nixpkgsJustin Bedo
2020-02-14add gdrive downloaderJustin Bedo
- fetch dbNSFP automatically via gdrive.pl
2020-02-09lastal: initJustin Bedo
2019-12-18add exec''Justin Bedo
2019-12-18lumpy: initJustin Bedo
2019-12-17delly: initJustin Bedo
2019-12-16manta: initJustin Bedo
2019-09-06xenomapper: initJustin Bedo
2019-08-15qsub: fix broken qsub treeJustin Bedo
2019-08-15hisat2: initJustin Bedo
2019-08-15SNVer: init 0.5.3Justin Bedo
2019-07-26make stripping more liberalJustin Bedo
Update the regex so that /nix/store* prefix doesn't have to match. To make sure we aren't overly general, we strip only bionix stages (i.e., -bionix suffix has to be present in the hash).
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
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