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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
2019-12-18lumpy: initJustin Bedo
2019-12-17delly: missing fileJustin Bedo
2019-12-17manta: make multithreaded and apply execution contextJustin Bedo
2019-12-17Fix shard testJustin Bedo
2019-12-17delly: initJustin Bedo
2019-12-16manta: initJustin Bedo
2019-12-12octopus: fix incorrect error messageJustin Bedo
2019-12-05platypus: remove debugging codeJustin Bedo
2019-11-29snpeff: GRCh37.87 -> GRCh37.75Justin Bedo
2019-11-27gridss: 2.7.2 → 2.7.3Justin Bedo
2019-11-20gridss: 2.7.1 → 2.7.2Justin Bedo
2019-11-04gridss: 2.7.0 → 2.7.1Justin Bedo
2019-11-01gridss: 2.6.2 -> 2.7.0Justin Bedo
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.
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