bh20-seq-resource/workflows/tools, branch yamlfa2ttl Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis http://git.systemreboot.net/bh20-seq-resource/atom?h=yamlfa2ttl 2021-01-06T08:34:14+00:00 Pubseq fetch: sometimes a request times out. So repeat with intervals. 2021-01-06T08:34:14+00:00 Pjotr Prins 2021-01-06T08:33:35+00:00 urn:sha1:c31835f787f3ae36e26bad0a1803f8557f8084e7 Fetching fixes 2021-01-05T13:13:15+00:00 Pjotr Prins 2021-01-05T13:13:15+00:00 urn:sha1:17cd8caa85991784f205109f2b64b255726a0e80 Add option for fetching fasta 2021-01-05T12:35:05+00:00 Pjotr Prins 2021-01-05T12:35:05+00:00 urn:sha1:ced9613aa1c18c6a68056d1898b69865beac9ac2 fetch: do a straight dump of the original record 2021-01-05T12:29:41+00:00 Pjotr Prins 2021-01-05T12:29:41+00:00 urn:sha1:2ceeccd5e5158362548b868390e9d411f73cd9ff fetches original metadata from PubSeq/Arvados 2021-01-05T12:07:39+00:00 Pjotr Prins 2021-01-05T12:07:39+00:00 urn:sha1:1187fa716cacde2b50566b67b5d619b8f12894f9 API: fix returned record to include original metadata 2021-01-05T09:34:26+00:00 Pjotr Prins 2021-01-05T09:34:26+00:00 urn:sha1:9d75ce088e6388bf23ae077fd06b2a3f51be1bda Rename 2021-01-05T07:11:13+00:00 Pjotr Prins 2021-01-05T07:11:13+00:00 urn:sha1:3c09a92423408d01b64e1b842c6b96778939d098 mapping: no longer requires specimen file for genbank output 2021-01-04T10:25:36+00:00 Pjotr Prins 2021-01-04T10:25:36+00:00 urn:sha1:f9f27a787fef0ad58c1ae465d8ba1ee4634083ae mapping sample_species using regex 2021-01-04T09:40:54+00:00 Pjotr Prins 2021-01-04T09:40:54+00:00 urn:sha1:3593b3f6a835f6c5927cbb1cc79e3db3c5d0053a Started on normalization 2021-01-04T08:58:38+00:00 Pjotr Prins 2021-01-04T08:58:38+00:00 urn:sha1:1c4e055b8a9dc53b7fdbdf12d4b0a7e877fbc2ef