bh20-seq-resource/bh20seqanalyzer, 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 2020-07-16T20:27:48+00:00 Add "validated" and "running workflows" tables to status 2020-07-16T20:27:48+00:00 Peter Amstutz 2020-07-16T20:27:32+00:00 urn:sha1:d49f6b5e11a41a51cb257bbafdcba410544f8486 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> Refactor analysis code into a class 2020-07-16T15:48:35+00:00 Peter Amstutz 2020-07-16T15:48:35+00:00 urn:sha1:53ff8af0843942d83dff9fd5b95d1ae98e80fe27 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Add --revalidate and fix checking/updating properties. 2020-07-08T20:16:42+00:00 Peter Amstutz 2020-07-08T20:16:42+00:00 urn:sha1:cd25f56f4d9aea1d30cc17ee923a6d8dd6c63e5a Get count from arvados 2020-07-08T19:18:00+00:00 Peter Amstutz 2020-07-08T18:02:11+00:00 urn:sha1:cbb191cb23f4e40b1a1d3024401960939fda9bc3 Separate pending/rejected tables "Lastest results" is latest successful run. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> --print-status=html creates html report 2020-07-07T21:17:59+00:00 Peter Amstutz 2020-07-07T21:17:31+00:00 urn:sha1:ba38aaf6920b246f6644cfb49730a5e2ee5f9db0 Add bh20-seq-analyzer --print-status 2020-07-05T21:33:26+00:00 Peter Amstutz 2020-07-05T21:33:26+00:00 urn:sha1:4f30e506055acb788a1ff1bbcb6359c4413a4eab Get status from new property "status: validated/rejected" Also store QC fail error message. A little more logging 2020-07-03T21:40:17+00:00 Peter Amstutz 2020-07-03T21:40:17+00:00 urn:sha1:dd0ff95c6973953542cc3a275be2b057b30ff577 Add --no-start-analysis 2020-07-03T21:20:28+00:00 Peter Amstutz 2020-07-03T21:20:28+00:00 urn:sha1:36f5c5b58a2de662eae9f379e66a9695d300dc2e Adjust QC filter and relabel output sequence with sample_id 2020-06-22T18:25:45+00:00 Peter Amstutz 2020-06-22T18:23:40+00:00 urn:sha1:76883d02e6073f990ea980dad1f8cf21121255ff