Age | Commit message (Collapse) | Author | |
---|---|---|---|
2024-11-12 | deprecate platypusHEADmaster | Justin Bedo | |
2024-10-31 | migrate zig code and target baseline cpu | Justin Bedo | |
2024-10-31 | bwa-mem2: 2.1 -> 2.2.1 | Justin Bedo | |
2024-06-04 | strip-store-paths: update to latest zig | Justin Bedo | |
2023-12-06 | strip-store-paths: update for latest zig | Justin Bedo | |
2023-10-10 | linkOutputs: fix shell interpretation of destination name | Justin Bedo | |
2023-10-10 | ampliconarchitect: init | Justin Bedo | |
2023-03-27 | samtools.queryRegion: queries regions from a fasta file | lezhou8 | |
Only the indexing functionality of samtools faidx is used, rather than also the region querying functionality. | |||
2023-02-27 | platypus.callVariants: strip platypus options from VCF output | lezhou8 | |
The detailed options embedded into the VCF reduces determinism, as it includes extranous details such as number of cores. | |||
2022-11-15 | fix missing flag in examples README | Justin Bedo | |
2022-10-24 | octopus.call: fix naming error in throw | Justin Bedo | |
2022-10-24 | samtools.view,mosdepth.depth: add targets parameter | Justin Bedo | |
2022-09-26 | last: align only a single fastq file | Justin Bedo | |
2022-08-23 | last: update for latest version | Justin Bedo | |
2022-06-19 | hatchet: include gurobi dependency if needed | Justin Bedo | |
2022-06-19 | quip: fix storing mates | Justin Bedo | |
2022-05-18 | quip: wrap in exec context | Justin Bedo | |
2022-05-16 | quip: init | Justin Bedo | |
2022-05-16 | HATCHet: 0.4.9 -> 0.4.14 | Justin Bedo | |
2022-03-09 | octopus: strip ARGV line to prevent huge closures | Justin Bedo | |
2022-02-28 | remove lumpy from testing | Justin Bedo | |
Deprecated upstream due to python2. | |||
2022-02-21 | linkOutputs: ignore null values | Justin Bedo | |
2022-02-09 | whisper: RG line support | Justin Bedo | |
2022-02-09 | whisper: fix sorting for sam output | Justin Bedo | |
2022-02-09 | don't strip store paths from bams | Justin Bedo | |
Due to BAM compression attempting to strip store paths is a waste of time. | |||
2022-02-08 | gridss: 2.13.1 -> 2.13.2 | Justin Bedo | |
2022-02-07 | pizzly: init | Justin Bedo | |
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 | |
2022-01-21 | linkOutputs: rewrite to use script instead of environment variable | Justin 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. | |||
2022-01-17 | 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 | strip-store-paths: allow no files | Justin Bedo | |
2022-01-06 | xenomapper: update location of package | Justin Bedo | |
2022-01-06 | strip: rollback simplification | Justin 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. | |||
2022-01-05 | gridss: 2.13.0 -> 2.13.1 | Justin Bedo | |
2022-01-05 | fix bug in strip-store-paths | Justin Bedo | |
also taking the opportunity to simplify the rewriteOutput function and handle filenames with spaces | |||
2022-01-04 | samtools-flagstat: fix name | Justin Bedo | |
2022-01-01 | update to zig 0.9.0 | Justin Bedo | |
2022-01-01 | update copyright year | Justin Bedo | |
2021-12-20 | rewrite strip store paths | Justin 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. | |||
2021-12-20 | 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). | |||
2021-12-18 | update dbNSFP hashes | Justin Bedo | |
these have changed‽ | |||
2021-12-14 | tests: test RG line functionality | Justin Bedo | |
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 | |