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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
2021-12-03genmap: initJustin Bedo
2021-11-25update readme link to tazjin's guideJustin Bedo
2021-11-25Fix typo in example READMEJustin Bedo
2021-11-23update contact information in READMEJustin Bedo
2021-11-03update ex-tnpair cluster exampleJustin Bedo
- fix bug with deprecated use of slurm tree - remove torque support
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
2021-10-08Update READMEJustin Bedo
1. Add citation to paper 2. Create a chat room on Matrix
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).
2021-06-25linkOutputs: passthrough the inputs to make it easier for downstream ↵Justin Bedo
expressions to refer to build products
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
2021-02-16Add -I flags to example invocationsJustin Bedo
BioNix is expected to be in the search path, which by default is not the case. Explicitly adding include flags to the build invocation in the examples simplifies execution for new users (issue #17).
2021-02-08refactor slurm implementation to allow for overlaysJustin Bedo
2021-02-08don't recursive update overlaysJustin Bedo
2021-02-08add flake.nixJustin Bedo
2021-02-03add inline documentationJustin Bedo
2021-02-03reinstate all testsJustin 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
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