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2020-04-23Merge pull request #33 from AndreaGuarracino/patch-9LLTommy
script updating
2020-04-23Merge pull request #32 from AndreaGuarracino/patch-10LLTommy
dictionaries updating and creation
2020-04-22code cleaning, checking and writing missing term on fileAndrea Guarracino
- the script checks for country and specimen_source - now the missing terms are written on a tsv file
2020-04-22created dict for host health statusAndrea Guarracino
2020-04-22added some rows in the speciesman dictAndrea Guarracino
2020-04-22added some rows in the ncbi_countries dictAndrea Guarracino
2020-04-22updated IDs list - 2020/04/22Andrea Guarracino
2020-04-22Fixing ShEx expression, one ? too muchlltommy
2020-04-22Forgot to add _idlltommy
2020-04-22updating example with ontology term for host_health_statuslltommy
2020-04-22Including restrictions to the host statuslltommy
2020-04-22Small changes all around, trying to make the importer/metadata betterlltommy
2020-04-22Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-22Merge pull request #31 from DCGenomics/patch-1LLTommy
Update metadata.yaml
2020-04-22Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-21Update metadata.yamlBen Busby
2020-04-21Increase ram requirement for minimap2Peter Amstutz
Add --kickoff to immediately start an analysis workflow. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Workaround CWL limit by chunking file listPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Work around CWL content size limit by chunkingPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21add noLinkCheck to specimen_source2Peter Amstutz
2020-04-21Tweak handling of "coverage" also fix typoPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Working on NCBI importPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21fixing silly mistakelltommy
2020-04-21Updated shex and manditory fields and stufflltommy
2020-04-20Add readsMergeDedup.fasta to outputPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Make sure there is a newline in relabeled fasta (but no blank lines)Peter Amstutz
2020-04-20Reconsidered these should be noLinkCheckPeter Amstutz
2020-04-20Add identity:true to collection_locationPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Schema changes from @LLTommyPeter Amstutz
2020-04-20Better handling of duplicate sequencesPeter Amstutz
Also save original fasta label in metadata
2020-04-20Relabel sequences to match metadata subjects.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Move workflows into main repoPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Add ShEx validationPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Merge pull request #29 from inutano/fix-mappingsLLTommy
fix MinION to ONT
2020-04-20Merge pull request #28 from AndreaGuarracino/patch-8LLTommy
fixed missing variable and managed comma in dicts
2020-04-20fix MinION to ONTTazro Inutano Ohta
2020-04-20Making collection date and collection location MANDATORY fields, turning ↵lltommy
orcid into IRI
2020-04-20Fixing string -> URI in speciman, plus other thingslltommy
2020-04-19added 'np/op' control for specimen_sourceAndrea Guarracino
2020-04-19Further updates to our NCBI dictonaries to translate this s*** to our modellltommy
2020-04-19fixed missing variable and managed comma in dictsAndrea Guarracino
2020-04-19small updates to the yaml schema, updating the example fileslltommy
2020-04-19Updating NCBI dictonaries, adding UI options, small yaml schema changeslltommy
2020-04-19Merge pull request #25 from AndreaGuarracino/patch-5Pjotr Prins
accession list 2020/04/18
2020-04-19Merge 984f74f7d7219c83d280b6eee46cba4aed4298bbPjotr Prins
2020-04-19Merge pull request #26 from AndreaGuarracino/patch-6Pjotr Prins
new script release
2020-04-19Merge branch 'master' into patch-6Pjotr Prins
2020-04-19Merge pull request #27 from AndreaGuarracino/patch-7Pjotr Prins
updated term-mapping dictionaries
2020-04-19Merge pull request #24 from adamnovak/dropdownsPjotr Prins
Add dropdown support to web uploader metadata form
2020-04-19Merge pull request #23 from AndreaGuarracino/patch-3Pjotr Prins
accessions list CoV-2 from NCBI Virus 2020/04/15
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