bh20-seq-resource/workflows, branch generate-cwl Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis http://git.systemreboot.net/bh20-seq-resource/atom?h=generate-cwl 2021-01-28T18:49:28+00:00 Restored tools submodule 2021-01-28T18:49:28+00:00 Pjotr Prins 2021-01-28T18:49:28+00:00 urn:sha1:78c597ca254c4fd1f484e8054d745fd011681dbc Moving tools out of submodules (sorry!) 2021-01-28T18:45:52+00:00 Pjotr Prins 2021-01-28T18:45:52+00:00 urn:sha1:8a7e79d6daa06da4d8ca2a391bae0a00124a2ed3 Add phylogeny workflow 2021-01-26T12:06:57+00:00 Njagi Mwaniki 2021-01-26T10:44:01+00:00 urn:sha1:4842117f530aba08b4a253aee533a8d4802b1c12 Signed-off-by: Njagi Mwaniki <njagi@urbanslug.com> GenBank: Fix normalization and depth differences with original records 2021-01-08T10:33:13+00:00 Pjotr Prins 2021-01-08T10:33:13+00:00 urn:sha1:b112b3203e34ea61dfdf802bce5036f938eaa774 Set JSON indentation 2021-01-08T07:48:14+00:00 Pjotr Prins 2021-01-08T07:48:14+00:00 urn:sha1:5d941e47e27a3cd2c47f8ee51f5523d180f8a5b2 Get correct GenBank ID with version, see #122 2021-01-08T07:34:04+00:00 Pjotr Prins 2021-01-08T07:34:04+00:00 urn:sha1:a9964da4a9efb1b068f80c0b632d0cc7bf923c58 FASTA file should not have leading space 2021-01-08T07:12:49+00:00 Pjotr Prins 2021-01-08T07:12:49+00:00 urn:sha1:97a820f250063d223007d3d8fea5901a1bfac77d Allow for xml and xml.gz files 2021-01-07T09:17:59+00:00 Pjotr Prins 2021-01-07T09:17:47+00:00 urn:sha1:329a1a7e122eda41016185d1b1e8d50d97f8857b cleaned utils.py 2021-01-06T13:13:13+00:00 AndreaGuarracino 2021-01-06T13:13:13+00:00 urn:sha1:27a2b926036211469eccbf8c3d9580182482bdc2 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