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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
2020-05-24gridss: 2.8.3 -> 2.9.1Justin Bedo
2020-05-24octopus: remove normal flagJustin Bedo
2020-04-27octopus: parameterise max-genotypes and targetsJustin Bedo
2020-04-22fix error message for linkOutputsJustin Bedo
2020-04-10gridss 2.7.3 -> 2.8.3Justin Bedo
2020-04-10update tnpair example to run on colo828Justin Bedo
2020-03-27update exampes to use nixpkgs.lib.pipeJustin 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
2020-02-03octopus-call: fix filetype typoJustin Bedo
2019-12-20kallisto: attempt at making determinsticJustin Bedo
2019-12-20lumpy: fix error messageJustin Bedo
2019-12-18add exec''Justin Bedo
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