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

Age	Commit message (Expand)	Author
2020-04-29	Use subprocess invocation is backwards compatible with Python 3.5	Peter Amstutz
2020-04-29	Add reference	Peter Amstutz
2020-04-28	Merge branch 'master' of https://github.com/arvados/bh20-seq-resource	lltommy
2020-04-28	Decision to settle for float instead of integers for the coverage	lltommy
2020-04-28	Call clustalw to compare sequence to reference	Peter Amstutz
2020-04-28	Changes to the structure - we use lists now instead of strings where it makes...	lltommy
2020-04-23	adding a submitter comment field	lltommy
2020-04-23	Adding a third sequence technology option	lltommy
2020-04-23	Merge branch 'master' into patch-3	LLTommy
2020-04-22	Fixing ShEx expression, one ? too much	lltommy
2020-04-22	Forgot to add _id	lltommy
2020-04-22	Including restrictions to the host status	lltommy
2020-04-22	Small changes all around, trying to make the importer/metadata better	lltommy
2020-04-21	Work around CWL content size limit by chunking	Peter Amstutz
2020-04-21	add noLinkCheck to specimen_source2	Peter Amstutz
2020-04-21	Tweak handling of "coverage" also fix typo	Peter Amstutz
2020-04-21	Working on NCBI import	Peter Amstutz
2020-04-21	Updated shex and manditory fields and stuff	lltommy
2020-04-20	Reconsidered these should be noLinkCheck	Peter Amstutz
2020-04-20	Add identity:true to collection_location	Peter Amstutz
2020-04-20	Schema changes from @LLTommy	Peter Amstutz
2020-04-20	Better handling of duplicate sequences	Peter Amstutz
2020-04-20	Make doc not contradict option list	Adam Novak
2020-04-20	Put back Intersex with the closest PATO equivalent	Adam Novak
2020-04-20	Add ShEx validation	Peter Amstutz
2020-04-20	Making collection date and collection location MANDATORY fields, turning orci...	lltommy
2020-04-20	Fixing string -> URI in speciman, plus other things	lltommy
2020-04-19	small updates to the yaml schema, updating the example files	lltommy
2020-04-19	Updating NCBI dictonaries, adding UI options, small yaml schema changes	lltommy
2020-04-19	Merge pull request #24 from adamnovak/dropdowns	Pjotr Prins
2020-04-18	Extending yaml schema a bit and adding additional information for the UI	lltommy
2020-04-17	Copy NCIT IRIs back to schema doc	Adam Novak
2020-04-17	Spruce up the options file and add missing values	Adam Novak
2020-04-17	Create option dropdowns from an options file	Adam Novak
2020-04-15	Typo: submitter_orchid -> submitter_orcid	Stian Soiland-Reyes
2020-04-15	Changing vaccination URI	lltommy
2020-04-15	Fixing small typo	lltommy
2020-04-15	relaxing regEx cause orichids can look like whatever it seems, not only numbers	lltommy
2020-04-14	Updated yaml schema and examples - plus ShEX shape to go along with it. Still...	lltommy
2020-04-13	Inject path to find module bh20sequploader	Pjotr Prins
2020-04-13	Add __init__.py and fix imports	Peter Amstutz
2020-04-13	Closes #5	Pjotr Prins
2020-04-13	Starting to turn values into IRIs ...	lltommy
2020-04-11	Adding noLinkCheck to root	lltommy
2020-04-11	Adding descriptions to the yml schema, slight changes to the yml schema	lltommy
2020-04-10	Propagating metadata to output works now.	Peter Amstutz
2020-04-10	Fix swapped fasta/fastq	Peter Amstutz
2020-04-10	Add qc_fasta	Peter Amstutz
2020-04-10	Fix up fasta/fastq validation	Peter Amstutz
2020-04-10	Validate & propagate metadata	Peter Amstutz