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

Age	Commit message (Expand)	Author
2020-07-08	Uploader checks for duplicates	Peter Amstutz
2020-07-08	Avoid redundant loading of schema	Peter Amstutz
2020-07-08	Hack in a valid-uri check	Peter Amstutz
2020-07-07	minimap2 returns nothing when there is no alignment.	Peter Amstutz
2020-07-07	Use minimap2 instead of clustalw for fasta QC	Peter Amstutz
2020-07-05	Add bh20-seq-analyzer --print-status	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
2020-07-03	Fix single arg upload	Peter Amstutz
2020-06-22	Better invalid sequence QC handling	Peter Amstutz
2020-06-22	Handle upload & assembly of gzipped, paired-end fastq	Peter Amstutz
2020-05-29	Changed doc comment in schema	Pjotr Prins
2020-05-29	Improved error output for the web uploader	Pjotr Prins
2020-05-28	Web: debugging metadata submission	Pjotr Prins
2020-05-28	Uploader: validate metadata first (it is faster)	Pjotr Prins
2020-05-06	Adding additional frontend option (PATO_0001340) to QC	lltommy
2020-04-30	Handle running in a container with no username	Peter Amstutz
2020-04-30	Last addition/edits to the meta data schema	lltommy
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