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AgeCommit message (Expand)Author
2020-08-28added control (locally and in the validation) that sample_id has to be the sa...AndreaGuarracino
2020-08-27updated dependency from clustalw to minimap2; the genbank script no longer cr...AndreaGuarracino
2020-08-26added option in the genbank script to ignore (already validated) IDs; code cl...AndreaGuarracino
2020-08-25the YAML/FASTA pair is not created for samples where at least one mandatory f...AndreaGuarracino
2020-08-24fixed protocol for the dictionary entries that caused validation problemsAndreaGuarracino
2020-08-23genbank/sra scripts update to be more generic with the specimen sourcesAndreaGuarracino
2020-08-23added new countries and speciesman sources: fixed few country entriesAndreaGuarracino
2020-08-22genbank/sra scripts updated to read the dictionaries in a more general wayAndreaGuarracino
2020-08-22lots of new dictionary termsAndreaGuarracino
2020-07-17Comment out some broken links for nowPeter Amstutz
2020-07-17Preparing for EBI submissionPjotr Prins
2020-07-17Started EBI submissionPjotr Prins
2020-07-16Report similarity == 0Peter Amstutz
2020-07-16Cleanup script also clears errors for revalidatePeter Amstutz
2020-07-16Catch exceptionsPeter Amstutz
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
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
2020-07-06renamed sra script; added seq technology in its additional information field ...AndreaGuarracino
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 missi...AndreaGuarracino
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
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 unexpecte...Andrea Guarracino
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
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