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2020-07-17Comment out some broken links for nowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-17Preparing for EBI submissionPjotr Prins
2020-07-17Started EBI submissionPjotr Prins
2020-07-16Report similarity == 0Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-16Cleanup script also clears errors for revalidatePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-16Catch exceptionsPeter Amstutz
Add script to cleanup bad uploads. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-12added a suffix to distinguish which script created the error/warning filesAndreaGuarracino
2020-07-10metadata with missing host_species are not createdAndreaGuarracino
2020-07-10an output file is created with the accessions for which no YAML file is createdAndreaGuarracino
2020-07-10updated metadata sourceAndreaGuarracino
2020-07-10other term for Homo sapiens (for SRA samples)Andrea Guarracino
2020-07-09fixed bug that lead to invalid sample_sequencing_technology valuesAndrea Guarracino
2020-07-07Merge pull request #90 from AndreaGuarracino/patch-21LLTommy
genbank and sra scripts update, new terms in the ontology dictionaries
2020-07-07fix missing authors #91AndreaGuarracino
2020-07-07minimap2 returns nothing when there is no alignment.Peter Amstutz
2020-07-07if the technology is not found, the YAML file is not created; managed longer ↵AndreaGuarracino
species strings
2020-07-06renamed sra script; added seq technology in its additional information field ↵AndreaGuarracino
if the term …
2020-07-06fix ncbi_countries dictionaryAndreaGuarracino
2020-07-06new terms in the ncbi_countries dictionaryAndrea Guarracino
2020-07-06added seq technology in its additional information field if the term is ↵AndreaGuarracino
missing in the dicts
2020-07-06updated SraExperimentPackage infoAndreaGuarracino
2020-07-06two more terms in the ncbi_sequencing_technology dictionaryAndrea Guarracino
2020-07-06fixed bugs in the download_sra_dataAndrea Guarracino
2020-07-06new terms in the sequencing_technology dictionaryAndrea Guarracino
2020-07-03Add upload.cwlPeter Amstutz
2020-07-03Improving genbank import workflowPeter Amstutz
2020-06-22very little readme for the scriptsAndrea Guarracino
2020-06-22added new script to prepare metadata of sra dataAndreaGuarracino
2020-06-22moved the genbank script in his specific directoryAndreaGuarracino
2020-06-22added new dictionary entriesAndreaGuarracino
2020-06-22little fix for specimen_sourceAndrea Guarracino
2020-06-22new entries for the EBI samplesAndreaGuarracino
2020-06-22corrected the wrong entitiesAndrea Guarracino
http instead of https entity instead of wiki
2020-06-22Handle upload & assembly of gzipped, paired-end fastqPeter Amstutz
2020-06-15virtuoso: remove graph before updatePjotr Prins
2020-06-12species dictionaryAndrea Guarracino
2020-06-12species are managed in another dictionary, try-catch added to avoid ↵Andrea Guarracino
unexpected stops
2020-06-07the script is more verbose; added other countriesAndreaGuarracino
2020-06-06fixed collection_location when it is not present in the dictionary termsAndreaGuarracino
2020-06-06fixed collection-date management using a parserAndreaGuarracino
2020-06-06fixed collection-date management; updated assembly info management for new IDsAndreaGuarracino
2020-05-31Added new speciesman sourcesAndrea Guarracino
2020-05-31Added new sequencing technologiesAndrea Guarracino
2020-05-31Added new countriesAndrea Guarracino
2020-05-31Added new species and specimen sourcesAndrea Guarracino
2020-05-31Updated the host_sex and host_age managementAndrea Guarracino
2020-05-31The NCBI Virus entries are updated automaticallyAndrea Guarracino
2020-05-20Virtuoso update in CRONPjotr Prins
2020-05-13Virtuoso uploader: always upload countries and labelsPjotr Prins
2020-05-13Virtuoso: split named graphsPjotr Prins
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