bh20-seq-resource/bh20seqanalyzer, branch fasta-subset-from-query Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis http://git.systemreboot.net/bh20-seq-resource/atom?h=fasta-subset-from-query 2020-11-09T21:55:33+00:00 Make it so "pangenome analysis" only runs collect-seqs. 2020-11-09T21:55:33+00:00 Peter Amstutz 2020-11-09T21:55:33+00:00 urn:sha1:b5143c79de268b844f3a6a63d92c6389b047f35e Will ensure that metadata is kept up to date. GFA isn't being generated. Will introduce new workflow that uses from_sparql to analyze a subset. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> added control (locally and in the validation) that sample_id has to be the same in the metadata and in the FASTA header #103 2020-08-28T09:16:24+00:00 AndreaGuarracino 2020-08-28T09:16:24+00:00 urn:sha1:3165a31e321cbf4641f9afdcbea511ee66f673bb Update links to reflect latest workflow 2020-08-20T14:43:43+00:00 Peter Amstutz 2020-08-20T14:43:43+00:00 urn:sha1:53bb39c7de934139ad9929ffb1b1772411233d80 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Consolidate steps to scale graph generation workflow 2020-08-19T20:31:38+00:00 Peter Amstutz 2020-08-19T19:19:07+00:00 urn:sha1:b3d2ccf951903ac0b7d717357fb1cccca26fbd15 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Make sure move_fastq_to_fasta_results gets everything 2020-07-17T18:55:19+00:00 Peter Amstutz 2020-07-17T18:55:19+00:00 urn:sha1:b34f5f42b9bd7a522b9d9b22d736998c4815d9e7 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> 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>