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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).
2019-07-08tests: add kallisto testJustin Bedo
2019-07-08ensembl: init gtf and gff3Justin Bedo
2019-07-08ensembl: abstract versionJustin 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.
2019-07-03mosdepth-plot: allow selection of what to plotJustin Bedo
Previously global output was plotted. A new control flag allows specification of what to plot.
2019-07-03facets: fix execution environmentJustin Bedo
2019-07-03octopus: initial functionsJustin Bedo
2019-06-21gridss: 2.2.2 -> 2.4.0Justin Bedo
2019-06-21bwa-mem2: initJustin Bedo
2019-06-21Add CNVkit testJustin 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.
2019-06-12grcm38: fix typo in name of ensembl transcriptsJustin Bedo
2019-06-11rewrite README documentationJustin Bedo
Significant expansion of README to include installation instructions and instructions on how to use with HPC.
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.
2019-06-11references: fix file mode (remove executable flag)Justin Bedo
2019-06-06Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2019-06-06picard-markDuplicates: fix input and output typesl-d-s
2019-06-04strip: handle non-buildCommand based stagesJustin Bedo
2019-05-30picard-markDuplicates: Check for _any_ sorting of inputl-d-s
2019-05-30Add picard-markDuplicates - need to handle sorting ambiguity.l-d-s
2019-05-30Merge branch 'add-picard' of mac2559:~/Projects/bionixl-d-s
2019-05-22Unested picard-markDuplicates.l-d-s
2019-05-21fastp: input filetypesJustin Bedo
2019-05-21fastp: split outputs and set filetypesJustin Bedo
2019-05-21Update README.mdl-d-s
2019-05-21Update README.mdl-d-s
2019-05-16example: pass bionix to call.nix pipelineJustin Bedo
2019-05-16slurm: renamed from sbatchJustin Bedo
2019-05-16sbatch: allow path specification for sallocJustin Bedo
2019-05-16stage: fix multicore tagging to work with derivation overridingJustin Bedo
2019-05-15edit example to support passing bionix as argumentJustin Bedo
2019-05-14strip: remove store paths from outputs to minimise closuresJustin 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-regex: split into separate file to fix exec issuesJustin Bedo
2019-05-02shard: missing fileJustin 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
2019-04-30Add examples and example READMEJustin Bedo
2019-04-30fix example data urls and hashesJustin Bedo
2019-04-30cleanup examples and stray filesJustin Bedo
2019-04-18sbatch: initial slurm implementationJustin Bedo
2019-04-17snap: initJustin Bedo
2019-04-12minimap2: typoJustin Bedo
2019-04-12minimap2: initJustin Bedo
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