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2019-09-25grch37: add dbsnpJustin Bedo
2019-09-25facets: assume sorted vcfJustin Bedo
2019-09-25gridss 2.6.0 → 2.6.2Justin Bedo
2019-09-25grch38.31 → grch38.32Justin Bedo
2019-09-25add grch37Justin Bedo
2019-09-10gridss: 2.5.2 -> 2.6.0Justin Bedo
2019-09-06strelka: default callSomatic to snvsJustin Bedo
2019-09-06strelka: also strip command line from outputJustin Bedo
2019-09-06cnvkit: use python2Justin Bedo
2019-09-06test: disable strelka somatic testJustin Bedo
2019-09-06strelka: change outputs and taggingJustin Bedo
This resolves an issue where overriding the strelka derivations would lose the filetype tags.
2019-09-06xenomapper: initJustin Bedo
2019-09-06CNVkit: split into multiple outputsJustin Bedo
cnvkit: restructure out to link to multioutputs
2019-08-29CNVkit: merge into nixpkgsJustin Bedo
2019-08-29gridss: 2.5.1 -> 2.5.2Justin Bedo
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.
2019-08-19snver: fix linkingJustin Bedo
2019-08-16mosdepth: fix renamingJustin Bedo
2019-08-16mosdepth: add testJustin Bedo
2019-08-15qsub: fix broken qsub treeJustin Bedo
2019-08-15gridss: 2.5.0 -> 2.5.1Justin Bedo
2019-08-15hisat2: initJustin Bedo
2019-08-15SNVer: init 0.5.3Justin Bedo
2019-07-28gridss: 2.4.0 -> 2.5.0Justin Bedo
2019-07-26Simplify exampleJustin 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).
2019-07-08tests: 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
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