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2024-11-12deprecate platypusHEADmasterJustin Bedo
2024-10-31bwa-mem2: 2.1 -> 2.2.1Justin Bedo
2023-10-10ampliconarchitect: initJustin Bedo
2023-03-27samtools.queryRegion: queries regions from a fasta filelezhou8
Only the indexing functionality of samtools faidx is used, rather than also the region querying functionality.
2023-02-27platypus.callVariants: strip platypus options from VCF outputlezhou8
The detailed options embedded into the VCF reduces determinism, as it includes extranous details such as number of cores.
2022-10-24octopus.call: fix naming error in throwJustin Bedo
2022-10-24samtools.view,mosdepth.depth: add targets parameterJustin Bedo
2022-09-26last: align only a single fastq fileJustin Bedo
2022-08-23last: update for latest versionJustin Bedo
2022-06-19hatchet: include gurobi dependency if neededJustin Bedo
2022-06-19quip: fix storing matesJustin Bedo
2022-05-18quip: wrap in exec contextJustin Bedo
2022-05-16quip: initJustin Bedo
2022-05-16HATCHet: 0.4.9 -> 0.4.14Justin Bedo
2022-03-09octopus: strip ARGV line to prevent huge closuresJustin Bedo
2022-02-09whisper: RG line supportJustin Bedo
2022-02-09whisper: fix sorting for sam outputJustin Bedo
2022-02-09don't strip store paths from bamsJustin Bedo
Due to BAM compression attempting to strip store paths is a waste of time.
2022-02-08gridss: 2.13.1 -> 2.13.2Justin Bedo
2022-02-07pizzly: initJustin Bedo
2022-02-07hatchet: initJustin Bedo
2022-01-25add tabix indexingJustin Bedo
2022-01-25add bgz support and fix nested compression supportJustin Bedo
2022-01-17snpeff.dbnsfp: paramterise fieldsJustin Bedo
2022-01-17octopus: allow targets to be derivationsJustin Bedo
2022-01-12gridss.filterSomatic: missing fileJustin Bedo
2022-01-12gridss: add somatic variant filteringJustin Bedo
2022-01-06xenomapper: update location of packageJustin Bedo
2022-01-05gridss: 2.13.0 -> 2.13.1Justin Bedo
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
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