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2022-02-21linkOutputs: ignore null valuesJustin Bedo
2022-02-07pizzly: initJustin Bedo
2022-02-07hatchet: initJustin Bedo
2022-01-21linkOutputs: rewrite to use script instead of environment variableJustin Bedo
Previous implementation had issues when linking large numbers of outputs due to large environment variables (buildCommand). This patch reimplements linkOutputs to place the linking commands in a script rather than hold the commands in an environment variable.
2022-01-06strip-store-paths: allow no filesJustin Bedo
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
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