index
:
bh20-seq-resource
analysis-refactor
fasta-subset-from-query
generate-cwl
master
new_assembly_method_field
pangenome_workflow_abpoa
upload-download-status
uuid-for-resource
yamlfa2ttl
Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis
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Author
2020-11-11
Conflict in guix-deploy
Pjotr Prins
2020-11-11
Deployment
Pjotr Prins
2020-11-11
Move files to correct folder
lltommy
2020-11-11
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
lltommy
2020-11-11
Adding covid death and covid cases per country as additional background infor...
lltommy
2020-11-11
create_sra_metadata script doesn't trick the quality control about missing da...
AndreaGuarracino
2020-11-10
virtuoso: no-cache
Pjotr Prins
2020-11-10
virtuoso: header change
Pjotr Prins
2020-11-10
virtuoso: Added a --no-cache option
Pjotr Prins
2020-11-08
Uploaded UTHSC sequences
Pjotr Prins
2020-11-08
UTHSC samples
Pjotr Prins
2020-11-06
Add country entries that miss coordinates
Pjotr Prins
2020-11-06
Country trouble shooting
Pjotr Prins
2020-11-06
Countries
Pjotr Prins
2020-11-06
Using correct wikidata geo link
Pjotr Prins
2020-11-06
Adding Tennessee items
Pjotr Prins
2020-11-06
UTHSC upload info
Pjotr Prins
2020-09-29
esr_samples script refactoring; added a reference of the esr_samples script i...
AndreaGuarracino
2020-09-28
new countries; updated genbank/sra scripts to manage more specimen sources
AndreaGuarracino
2020-09-28
genbank and sra scripts more picky on the ontologies; added utils.py for shar...
AndreaGuarracino
2020-09-27
Virtuoso uploader: instructions
Pjotr Prins
2020-09-27
Virtuoso uploader: explicit output
Pjotr Prins
2020-09-27
Fixing missing dot in .ttl file
lltommy
2020-09-27
Adding script supporting semantic enrichment
lltommy
2020-09-26
script for processing the metadata of the ESR samples; moved delete_entries_o...
AndreaGuarracino
2020-09-25
added new New Zealand entries
AndreaGuarracino
2020-09-04
fixed bugs in in index management and type conversion
AndreaGuarracino
2020-09-04
sra script re-enabled, ready for tests
AndreaGuarracino
2020-09-04
added in the sra script an option to include only a subset of ids
AndreaGuarracino
2020-09-04
sra script updated for managing more locations
AndreaGuarracino
2020-09-04
synchronized the create_sra_metadata.py script with the latest updates
AndreaGuarracino
2020-08-29
fixed few countries ontology terms; added a new species
AndreaGuarracino
2020-08-28
added control (locally and in the validation) that sample_id has to be the sa...
AndreaGuarracino
2020-08-27
updated dependency from clustalw to minimap2; the genbank script no longer cr...
AndreaGuarracino
2020-08-26
added option in the genbank script to ignore (already validated) IDs; code cl...
AndreaGuarracino
2020-08-25
the YAML/FASTA pair is not created for samples where at least one mandatory f...
AndreaGuarracino
2020-08-24
fixed protocol for the dictionary entries that caused validation problems
AndreaGuarracino
2020-08-23
genbank/sra scripts update to be more generic with the specimen sources
AndreaGuarracino
2020-08-23
added new countries and speciesman sources: fixed few country entries
AndreaGuarracino
2020-08-22
genbank/sra scripts updated to read the dictionaries in a more general way
AndreaGuarracino
2020-08-22
lots of new dictionary terms
AndreaGuarracino
2020-07-17
Comment out some broken links for now
Peter Amstutz
2020-07-17
Preparing for EBI submission
Pjotr Prins
2020-07-17
Started EBI submission
Pjotr Prins
2020-07-16
Report similarity == 0
Peter Amstutz
2020-07-16
Cleanup script also clears errors for revalidate
Peter Amstutz
2020-07-16
Catch exceptions
Peter Amstutz
2020-07-12
added a suffix to distinguish which script created the error/warning files
AndreaGuarracino
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
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