| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2020-04-28 | updated to manage list fields and added new control on nasopharyngeal/throat ↵ | Andrea Guarracino | |
| swab | |||
| 2020-04-28 | Changes to the structure - we use lists now instead of strings where it ↵ | lltommy | |
| makes sense. This allows us to have multiple values where in makes sense | |||
| 2020-04-23 | code cleaning, refactoring, submitter name and address | Andrea Guarracino | |
| - additional_submitter_information for information not equal to name or address - added another check for coverage | |||
| 2020-04-22 | code cleaning, checking and writing missing term on file | Andrea Guarracino | |
| - the script checks for country and specimen_source - now the missing terms are written on a tsv file | |||
| 2020-04-22 | Small changes all around, trying to make the importer/metadata better | lltommy | |
| 2020-04-21 | Tweak handling of "coverage" also fix typo | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-21 | Working on NCBI import | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-21 | Updated shex and manditory fields and stuff | lltommy | |
| 2020-04-19 | added 'np/op' control for specimen_source | Andrea Guarracino | |
| 2020-04-19 | fixed missing variable and managed comma in dicts | Andrea Guarracino | |
| 2020-04-18 | new script release | Andrea Guarracino | |
| - now the script is more gentle with the server, requesting metadata in batches, reducing the ovrall execution time; - in the YAML files are created field for sample_sequencing_technology, sample_sequencing_technology2, sample_sequencing_technology3, specimen_source, and specimen_source2; - in sequencing_coverage stuff like 'x', 'X', etc... is stripped, and the ',' replaced by '.'; - the script exploits the dictionaries in the /scripts/dict_ontology_standardization. Now I have used ncbi_specesman_source.csv, ncbi_sequencing_technology.csv, and ncbi_countries.csv. - in ncbi_sequencing_technology.csv I've added 'Oxford Nanopore' and 'MinION Oxford Nanopore' - for specimen_source, when there is one of 'NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', or 'np/np swab', I put both of them. | |||
| 2020-04-14 | Rename script/from_genbank_to_fasta_and_yaml.py to ↵ | Andrea Guarracino | |
| scripts/from_genbank_to_fasta_and_yaml.py | |||
 |
index : bh20-seq-resource | |
| Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis |
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