bionix.git/tools, branch masterFunctional, highly-reproducible bioinformatics pipelineshttps://vk3.wtf/cgit/bionix.git/atom/tools?h=master2024-11-12T04:50:42Zdeprecate platypus2024-11-12T04:50:42ZJustin Bedocu@cua0.org2024-11-12T04:50:42Zurn:sha1:58fa67ffd09d3bdfe72bef7c873ef94190dc6708bwa-mem2: 2.1 -> 2.2.12024-10-31T02:57:42ZJustin Bedocu@cua0.org2024-10-31T02:52:24Zurn:sha1:824deda0e1a7e46d4e17ff3e472dcddec220b308ampliconarchitect: init2023-10-10T02:26:17ZJustin Bedocu@cua0.org2023-05-25T01:50:52Zurn:sha1:7372c27ea3930ad464b05a6c3ab4fd6348eb3abdsamtools.queryRegion: queries regions from a fasta file2023-03-27T23:01:10Zlezhou8lezhou@protonmail.com2023-03-24T00:15:50Zurn:sha1:59edb7d9c37a688c8c408508c1a9ae5d37df348f
Only the indexing functionality of samtools faidx is used, rather than also the region querying functionality.
platypus.callVariants: strip platypus options from VCF output2023-02-27T02:45:10Zlezhou8lezhou@protonmail.com2023-01-30T01:37:39Zurn:sha1:4ef81f5f631f5766287d3bbcb6bd1238259f0523
The detailed options embedded into the VCF reduces determinism, as it
includes extranous details such as number of cores.
octopus.call: fix naming error in throw2022-10-24T02:37:57ZJustin Bedocu@cua0.org2022-10-24T02:36:31Zurn:sha1:1a7ed52d1b3de6e1e7c8525cca3333c06930b90asamtools.view,mosdepth.depth: add targets parameter2022-10-24T02:37:57ZJustin Bedocu@cua0.org2022-09-26T01:51:52Zurn:sha1:36a0a03eda2ec8cf9b1f5fea8c437b68638d1de5last: align only a single fastq file2022-09-26T01:51:52ZJustin Bedocu@cua0.org2022-08-23T08:36:40Zurn:sha1:81cfa50e6b345942951b68eac0e184ea025f2ae4last: update for latest version2022-08-23T08:36:28ZJustin Bedocu@cua0.org2022-08-23T08:36:28Zurn:sha1:5107449eeb29963b98cb5b6ded6418d930590c23hatchet: include gurobi dependency if needed2022-06-18T22:31:23ZJustin Bedocu@cua0.org2022-06-18T22:27:00Zurn:sha1:2d7a2b001936a8a047118af0f99a9cbfd38d258a