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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.
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
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