bh20-seq-resource - Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis

Age	Commit message (Expand)	Author
2020-07-12	Generate About page	Pjotr Prins
2020-07-12	Docs: started on metadata modification	Pjotr Prins
2020-07-12	CounterDB	Pjotr Prins
2020-07-12	About page: add Andrea and Erik; add CC0 license link	Pjotr Prins
2020-07-12	Remove duplicate counter	Pjotr Prins
2020-07-12	Remove duplicate counter	Pjotr Prins
2020-07-12	Remove duplicate counter	Pjotr Prins
2020-07-10	metadata with missing host_species are not created	AndreaGuarracino
2020-07-10	an output file is created with the accessions for which no YAML file is created	AndreaGuarracino
2020-07-10	updated metadata source	AndreaGuarracino
2020-07-10	other term for Homo sapiens (for SRA samples)	Andrea Guarracino
2020-07-09	Skip certificate check - this was upstreamed in Arvados, so we can remove later	Pjotr Prins
2020-07-09	Merge pull request #93 from AndreaGuarracino/patch-22	Pjotr Prins
2020-07-09	fixed bug that lead to invalid sample_sequencing_technology values	Andrea Guarracino
2020-07-08	Adding missing GPS coordinates et all	lltommy
2020-07-08	Try to fix lab_address wrong predicate, fix submitter shape on the way and ho...	lltommy
2020-07-08	Merge pull request #92 from arvados/upload-download-status	Peter Amstutz
2020-07-08	Give uploader an option to trust local validation (for batch imports)upload-download-status	Peter Amstutz
2020-07-08	Uploader checks for duplicates	Peter Amstutz
2020-07-08	Avoid redundant loading of schema	Peter Amstutz
2020-07-08	Add --revalidate and fix checking/updating properties.	Peter Amstutz
2020-07-08	Hack in a valid-uri check	Peter Amstutz
2020-07-08	Get count from arvados	Peter Amstutz
2020-07-08	Fetch status as anonymous user	Peter Amstutz
2020-07-08	Split upload tab. Add upload status tab.	Peter Amstutz
2020-07-08	Merge pull request #89 from proccaserra/patch-1	LLTommy
2020-07-07	Merge branch 'master' of https://github.com/arvados/bh20-seq-resource	lltommy
2020-07-07	Adding some more country labels. Some GPS are still missing, will handle in t...	lltommy
2020-07-07	Adding sequencer labels	lltommy
2020-07-07	Merge pull request #90 from AndreaGuarracino/patch-21	LLTommy
2020-07-07	--print-status=html creates html report	Peter Amstutz
2020-07-07	fix missing authors #91	AndreaGuarracino
2020-07-07	minimap2 returns nothing when there is no alignment.	Peter Amstutz
2020-07-07	if the technology is not found, the YAML file is not created; managed longer ...	AndreaGuarracino
2020-07-07	Use minimap2 instead of clustalw for fasta QC	Peter Amstutz
2020-07-06	renamed sra script; added seq technology in its additional information field ...	AndreaGuarracino
2020-07-06	fix ncbi_countries dictionary	AndreaGuarracino
2020-07-06	new terms in the ncbi_countries dictionary	Andrea Guarracino
2020-07-06	added seq technology in its additional information field if the term is missi...	AndreaGuarracino
2020-07-06	updated SraExperimentPackage info	AndreaGuarracino
2020-07-06	two more terms in the ncbi_sequencing_technology dictionary	Andrea Guarracino
2020-07-06	fixed bugs in the download_sra_data	Andrea Guarracino
2020-07-06	new terms in the sequencing_technology dictionary	Andrea Guarracino
2020-07-05	Add bh20-seq-analyzer --print-status	Peter Amstutz
2020-07-03	A little more logging	Peter Amstutz
2020-07-03	Add upload.cwl	Peter Amstutz
2020-07-03	Add --no-start-analysis	Peter Amstutz
2020-07-03	Add --skip-qc for faster batch import	Peter Amstutz
2020-07-03	Adding --skip-qc	Peter Amstutz
2020-07-03	Fix qc_fasta bug closing stream.	Peter Amstutz