bh20-seq-resource/scripts, branch analysis-refactor Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis http://git.systemreboot.net/bh20-seq-resource/atom?h=analysis-refactor 2020-07-16T18:28:02+00:00 Cleanup script also clears errors for revalidate 2020-07-16T18:28:02+00:00 Peter Amstutz 2020-07-16T18:28:02+00:00 urn:sha1:474d15e17be63046a091615e89ba63adecdb109b Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Catch exceptions 2020-07-16T16:33:07+00:00 Peter Amstutz 2020-07-16T16:32:43+00:00 urn:sha1:6bfefe984a84fb215d61e045c49a4ab123bb7339 Add script to cleanup bad uploads. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> added a suffix to distinguish which script created the error/warning files 2020-07-12T13:58:29+00:00 AndreaGuarracino 2020-07-12T13:58:29+00:00 urn:sha1:bb90f06da570624952d4b7001ee37fc7018e3a7d metadata with missing host_species are not created 2020-07-10T13:39:02+00:00 AndreaGuarracino 2020-07-10T13:39:02+00:00 urn:sha1:2eab71a70b8630649303a9319e1baf9fa06f8ab4 an output file is created with the accessions for which no YAML file is created 2020-07-10T11:55:49+00:00 AndreaGuarracino 2020-07-10T11:55:49+00:00 urn:sha1:8cb542fdf60273aec7ec107f8bc4896375381263 updated metadata source 2020-07-10T11:43:59+00:00 AndreaGuarracino 2020-07-10T11:43:59+00:00 urn:sha1:1655762b516804dad3d71538e95d97d74653c3e9 other term for Homo sapiens (for SRA samples) 2020-07-10T09:50:06+00:00 Andrea Guarracino 2020-07-10T09:50:06+00:00 urn:sha1:87e634040767373309fd7eb99784de0537f72059 fixed bug that lead to invalid sample_sequencing_technology values 2020-07-08T22:39:48+00:00 Andrea Guarracino 2020-07-08T22:39:48+00:00 urn:sha1:6207501c9b504936a61f232d33344e04350b0aed Merge pull request #90 from AndreaGuarracino/patch-21 2020-07-07T21:27:43+00:00 LLTommy 2020-07-07T21:27:43+00:00 urn:sha1:b994b59963248a301e1248f792f21d9ab2ea8a3f genbank and sra scripts update, new terms in the ontology dictionaries fix missing authors #91 2020-07-07T21:01:48+00:00 AndreaGuarracino 2020-07-07T21:01:48+00:00 urn:sha1:f77e86dbb84baf8add3d7a71f8f06fb44a99507b