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
2020-09-27
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
2020-07-10
updated metadata source
AndreaGuarracino
2020-07-10
other term for Homo sapiens (for SRA samples)
Andrea Guarracino
2020-07-09
fixed bug that lead to invalid sample_sequencing_technology values
Andrea Guarracino
2020-07-07
Merge pull request #90 from AndreaGuarracino/patch-21
LLTommy
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
2020-07-06
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
2020-07-03
Add upload.cwl
Peter Amstutz
2020-07-03
Improving genbank import workflow
Peter Amstutz
2020-06-22
very little readme for the scripts
Andrea Guarracino
2020-06-22
added new script to prepare metadata of sra data
AndreaGuarracino
2020-06-22
moved the genbank script in his specific directory
AndreaGuarracino
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