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2021-10-08Update READMEJustin Bedo
1. Add citation to paper 2. Create a chat room on Matrix
2021-09-21gridss: specify cores for all multithreaded phasesJustin Bedo
2021-09-16gridss: 2.12.0 -> 2.12.1Justin Bedo
2021-08-25fastp: use nixpkgs versionJustin Bedo
2021-08-02gridss: drop softclip to split read conversionJustin Bedo
Unnecessary if aligner supports split reads. Best to leave to user to manage.
2021-07-28bugfix: use unsorted type for alignment outputJustin Bedo
Most aligners are only pseudo-name sorted (i.e., pairs adjacant).
2021-06-25linkOutputs: passthrough the inputs to make it easier for downstream ↵Justin Bedo
expressions to refer to build products
2021-05-25gridss: 2.11.1 -> 2.12.0Justin Bedo
2021-04-20gridss: 2.10.2 -> 2.11.1Justin Bedo
2021-03-08facets: use tagged version of pctGCdataJustin Bedo
2021-02-23samtools-view: support specifying outfmt via stringsJustin Bedo
2021-02-19samtools-index: support cram indexingJustin Bedo
2021-02-16Add -I flags to example invocationsJustin Bedo
BioNix is expected to be in the search path, which by default is not the case. Explicitly adding include flags to the build invocation in the examples simplifies execution for new users (issue #17).
2021-02-08refactor slurm implementation to allow for overlaysJustin Bedo
2021-02-08don't recursive update overlaysJustin Bedo
2021-02-08add flake.nixJustin Bedo
2021-02-03add inline documentationJustin Bedo
2021-02-03reinstate all testsJustin Bedo
2021-02-03bwa-mem2: 2.0 -> 2.1Justin Bedo
2021-01-25kallisto-quant: strip call form run infoJustin Bedo
2021-01-20facets: 0.5.14 -> 0.6.1Justin Bedo
2021-01-19Update README.mdMatthew Wakefield
correct install string for Nix
2020-12-21snpeff: dbnsfp updateJustin Bedo
2020-12-14gridss: 2.10.1 -> 2.10.2Justin Bedo
2020-11-30gridss.assemble: fix workdir manipulationJustin Bedo
2020-11-18add encode blacklist to referencesJustin Bedo
2020-11-18rewrite cluster example to usse overlayJustin Bedo
2020-11-18switch to unchecked ADTsJustin Bedo
Checked ADTs are causing an issue with the new overlays. If an overlay that provides the entire tree is used, e.g.,: (self: super: super.slurm {}) then the result is unusable due to ADT type checking errors.
2020-11-17implement overlaysJustin Bedo
2020-11-16sambamba: initJustin Bedo
2020-11-03update example to not use explicit path referenceJustin Bedo
2020-11-02star: initJustin Bedo
2020-11-02gridss: 2.10.0 -> 2.10.1Justin Bedo
2020-10-15gridss: 2.9.4 -> 2.10.0Justin Bedo
2020-10-13mutect: fix app expression and tag output as vcfJustin Bedo
2020-09-02gridss: shard assembly into 10 pieces by defaultJustin Bedo
2020-09-02gridss: add missing flags parameterJustin Bedo
2020-08-25whisper: app expression merged into nixpkgsJustin Bedo
2020-08-09Update README.mdJustin Bedő
2020-08-10hisat2: add index prefixJustin Bedo
2020-08-10bwa: alt regex generalisationJustin Bedo
2020-08-10bwa2: update to releaseJustin Bedo
2020-07-16gridss: 2.9.1 -> 2.9.4Justin Bedo
2020-07-08cnvkit: python 2 -> python 3Justin Bedo
2020-06-27whisper: missing app expressionJustin Bedo
2020-06-27whisper: init 2.0Justin Bedo
2020-06-27octopus: write evidence bams to multioutputJustin Bedo
2020-06-23qsub,slurm: fix string escaping bugJustin Bedo
escapeShellArgs calls toString on the passed item, which for paths converts it to a string containing the full path outside the nix store. Avoid this by calling escapeShellArg on strings only.
2020-06-05facets: 0.5.6 -> 0.5.14Justin Bedo
2020-06-02samtools-merge: noop if only a single fileJustin Bedo
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