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3 daysdeprecate platypusHEADmasterJustin Bedo
2024-10-31migrate zig code and target baseline cpuJustin Bedo
2024-10-31bwa-mem2: 2.1 -> 2.2.1Justin Bedo
2024-06-04strip-store-paths: update to latest zigJustin Bedo
2023-12-06strip-store-paths: update for latest zigJustin Bedo
2023-10-10linkOutputs: fix shell interpretation of destination nameJustin 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.
2022-11-15fix missing flag in examples READMEJustin Bedo
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
2022-02-28remove lumpy from testingJustin Bedo
Deprecated upstream due to python2.
2022-02-21linkOutputs: ignore null valuesJustin 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
2022-01-21linkOutputs: rewrite to use script instead of environment variableJustin Bedo
Previous implementation had issues when linking large numbers of outputs due to large environment variables (buildCommand). This patch reimplements linkOutputs to place the linking commands in a script rather than hold the commands in an environment variable.
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
2022-01-06strip-store-paths: allow no filesJustin Bedo
2022-01-06xenomapper: update location of packageJustin Bedo
2022-01-06strip: rollback simplificationJustin Bedo
Fails sometimes when output is not a directory. This patch reverts to the previous implementation, but also patches in a fix for file names containing spaces.
2022-01-05gridss: 2.13.0 -> 2.13.1Justin Bedo
2022-01-05fix bug in strip-store-pathsJustin Bedo
also taking the opportunity to simplify the rewriteOutput function and handle filenames with spaces
2022-01-04samtools-flagstat: fix nameJustin Bedo
2022-01-01update to zig 0.9.0Justin Bedo
2022-01-01update copyright yearJustin Bedo
2021-12-20rewrite strip store pathsJustin Bedo
Old version used sed, which is not inplace and causes issues when garbage collection triggers during a build. This patch adds a small rewriter that works in place.
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).
2021-12-18update dbNSFP hashesJustin Bedo
these have changed‽
2021-12-14tests: test RG line functionalityJustin Bedo
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
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