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2022-01-04samtools-flagstat: fix nameJustin Bedo
2021-12-20facets.callCNV: refactor interfaceJustin Bedo
The VCF really is part of config as it's not variants called on the sample but population variants (like dbsnp).
2021-12-14subread: initJustin Bedo
2021-12-06parameterise RG line as nix attribute setJustin Bedo
Allows more seamless transitioning between alingment algorithms
2021-12-06gridss: 2.12.2 -> 2.13.0Justin Bedo
2021-12-03genmap: initJustin Bedo
2021-10-29treewide reformatting and simplificationJustin Bedo
- simplify with statix - reformat with nixpkgs-fmt
2021-10-29octopus: write region lists to region filesJustin Bedo
2021-10-14gridss: 2.12.0 -> 2.12.2Justin Bedo
2021-10-14Revert "gridss: 2.12.0 -> 2.12.1"Justin Bedo
This reverts commit 1ff1c9cf0bcc95a6555d1217598f55b7b9eae866. As per github release page: DO NOT USE: this release has a critical bug in the preprocessing step that removes all split reads
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).
2021-05-25gridss: 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
2021-02-03add inline documentationJustin 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
2020-12-14gridss: 2.10.1 -> 2.10.2Justin Bedo
2020-11-30gridss.assemble: fix workdir manipulationJustin Bedo
2020-11-16sambamba: initJustin 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
2020-08-10hisat2: 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
2020-06-05facets: 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
2020-04-10gridss 2.7.3 -> 2.8.3Justin Bedo
2020-02-09lastal: initJustin Bedo
2020-02-03octopus-call: fix filetype typoJustin Bedo
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