Age | Commit message (Collapse) | Author | |
---|---|---|---|
2022-02-07 | hatchet: init | Justin Bedo | |
2022-01-25 | add tabix indexing | Justin Bedo | |
2022-01-25 | add bgz support and fix nested compression support | Justin Bedo | |
2022-01-17 | snpeff.dbnsfp: paramterise fields | Justin Bedo | |
2022-01-17 | octopus: allow targets to be derivations | Justin Bedo | |
2022-01-12 | gridss.filterSomatic: missing file | Justin Bedo | |
2022-01-12 | gridss: add somatic variant filtering | Justin Bedo | |
2022-01-06 | xenomapper: update location of package | Justin Bedo | |
2022-01-05 | gridss: 2.13.0 -> 2.13.1 | Justin Bedo | |
2022-01-04 | samtools-flagstat: fix name | Justin Bedo | |
2021-12-20 | facets.callCNV: refactor interface | Justin Bedo | |
The VCF really is part of config as it's not variants called on the sample but population variants (like dbsnp). | |||
2021-12-14 | subread: init | Justin Bedo | |
2021-12-06 | parameterise RG line as nix attribute set | Justin Bedo | |
Allows more seamless transitioning between alingment algorithms | |||
2021-12-06 | gridss: 2.12.2 -> 2.13.0 | Justin Bedo | |
2021-12-03 | genmap: init | Justin Bedo | |
2021-10-29 | treewide reformatting and simplification | Justin Bedo | |
- simplify with statix - reformat with nixpkgs-fmt | |||
2021-10-29 | octopus: write region lists to region files | Justin Bedo | |
2021-10-14 | gridss: 2.12.0 -> 2.12.2 | Justin Bedo | |
2021-10-14 | Revert "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 | |||
2021-09-21 | gridss: specify cores for all multithreaded phases | Justin Bedo | |
2021-09-16 | gridss: 2.12.0 -> 2.12.1 | Justin Bedo | |
2021-08-25 | fastp: use nixpkgs version | Justin Bedo | |
2021-08-02 | gridss: drop softclip to split read conversion | Justin Bedo | |
Unnecessary if aligner supports split reads. Best to leave to user to manage. | |||
2021-07-28 | bugfix: use unsorted type for alignment output | Justin Bedo | |
Most aligners are only pseudo-name sorted (i.e., pairs adjacant). | |||
2021-05-25 | gridss: 2.11.1 -> 2.12.0 | Justin Bedo | |
2021-04-20 | gridss: 2.10.2 -> 2.11.1 | Justin Bedo | |
2021-03-08 | facets: use tagged version of pctGCdata | Justin Bedo | |
2021-02-23 | samtools-view: support specifying outfmt via strings | Justin Bedo | |
2021-02-19 | samtools-index: support cram indexing | Justin Bedo | |
2021-02-03 | add inline documentation | Justin Bedo | |
2021-02-03 | bwa-mem2: 2.0 -> 2.1 | Justin Bedo | |
2021-01-25 | kallisto-quant: strip call form run info | Justin Bedo | |
2021-01-20 | facets: 0.5.14 -> 0.6.1 | Justin Bedo | |
2020-12-14 | gridss: 2.10.1 -> 2.10.2 | Justin Bedo | |
2020-11-30 | gridss.assemble: fix workdir manipulation | Justin Bedo | |
2020-11-16 | sambamba: init | Justin Bedo | |
2020-11-02 | star: init | Justin Bedo | |
2020-11-02 | gridss: 2.10.0 -> 2.10.1 | Justin Bedo | |
2020-10-15 | gridss: 2.9.4 -> 2.10.0 | Justin Bedo | |
2020-10-13 | mutect: fix app expression and tag output as vcf | Justin Bedo | |
2020-09-02 | gridss: shard assembly into 10 pieces by default | Justin Bedo | |
2020-09-02 | gridss: add missing flags parameter | Justin Bedo | |
2020-08-25 | whisper: app expression merged into nixpkgs | Justin Bedo | |
2020-08-10 | hisat2: add index prefix | Justin Bedo | |
2020-08-10 | bwa: alt regex generalisation | Justin Bedo | |
2020-08-10 | bwa2: update to release | Justin Bedo | |
2020-07-16 | gridss: 2.9.1 -> 2.9.4 | Justin Bedo | |
2020-07-08 | cnvkit: python 2 -> python 3 | Justin Bedo | |
2020-06-27 | whisper: missing app expression | Justin Bedo | |
2020-06-27 | whisper: init 2.0 | Justin Bedo | |