Age | Commit message (Collapse) | Author | |
---|---|---|---|
2021-12-06 | gridss: 2.12.2 -> 2.13.0 | Justin Bedo | |
2021-12-03 | genmap: init | Justin Bedo | |
2021-11-25 | update readme link to tazjin's guide | Justin Bedo | |
2021-11-25 | Fix typo in example README | Justin Bedo | |
2021-11-23 | update contact information in README | Justin Bedo | |
2021-11-03 | update ex-tnpair cluster example | Justin Bedo | |
- fix bug with deprecated use of slurm tree - remove torque support | |||
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 | |||
2021-10-08 | Update README | Justin Bedo | |
1. Add citation to paper 2. Create a chat room on Matrix | |||
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). | |||
2021-06-25 | linkOutputs: passthrough the inputs to make it easier for downstream ↵ | Justin Bedo | |
expressions to refer to build products | |||
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 | |
2021-02-16 | Add -I flags to example invocations | Justin 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). | |||
2021-02-08 | refactor slurm implementation to allow for overlays | Justin Bedo | |
2021-02-08 | don't recursive update overlays | Justin Bedo | |
2021-02-08 | add flake.nix | Justin Bedo | |
2021-02-03 | add inline documentation | Justin Bedo | |
2021-02-03 | reinstate all tests | 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 | |
2021-01-19 | Update README.md | Matthew Wakefield | |
correct install string for Nix | |||
2020-12-21 | snpeff: dbnsfp update | Justin Bedo | |
2020-12-14 | gridss: 2.10.1 -> 2.10.2 | Justin Bedo | |
2020-11-30 | gridss.assemble: fix workdir manipulation | Justin Bedo | |
2020-11-18 | add encode blacklist to references | Justin Bedo | |
2020-11-18 | rewrite cluster example to usse overlay | Justin Bedo | |
2020-11-18 | switch to unchecked ADTs | Justin Bedo | |
Checked ADTs are causing an issue with the new overlays. If an overlay that provides the entire tree is used, e.g.,: (self: super: super.slurm {}) then the result is unusable due to ADT type checking errors. | |||
2020-11-17 | implement overlays | Justin Bedo | |
2020-11-16 | sambamba: init | Justin Bedo | |
2020-11-03 | update example to not use explicit path reference | 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 | |
2020-08-09 | Update README.md | Justin Bedő | |
2020-08-10 | hisat2: add index prefix | Justin Bedo | |