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2020-09-28new countries; updated genbank/sra scripts to manage more specimen sourcesAndreaGuarracino
2020-09-28genbank and sra scripts more picky on the ontologies; added utils.py for ↵AndreaGuarracino
shared functions
2020-09-27Virtuoso uploader: instructionsPjotr Prins
2020-09-27Virtuoso uploader: explicit outputPjotr Prins
2020-09-27Fixing missing dot in .ttl filelltommy
2020-09-27Adding script supporting semantic enrichmentlltommy
2020-09-27Adding a few labels to other used vocabslltommy
2020-09-27Updated country labels and GPS coordinateslltommy
2020-09-26script for processing the metadata of the ESR samples; moved ↵AndreaGuarracino
delete_entries_on_arvados script in scripts directory
2020-09-25added new New Zealand entriesAndreaGuarracino
2020-09-05increased the quality filter thresholdAndreaGuarracino
2020-09-04fixed bugs in in index management and type conversionAndreaGuarracino
2020-09-04sra script re-enabled, ready for testsAndreaGuarracino
2020-09-04added in the sra script an option to include only a subset of idsAndreaGuarracino
2020-09-04sra script updated for managing more locationsAndreaGuarracino
2020-09-04synchronized the create_sra_metadata.py script with the latest updatesAndreaGuarracino
2020-08-29fixed few countries ontology terms; added a new speciesAndreaGuarracino
2020-08-28added script to remove entries on ArvadosAndreaGuarracino
2020-08-28local QC is optionalAndreaGuarracino
2020-08-28added control (locally and in the validation) that sample_id has to be the ↵AndreaGuarracino
same in the metadata and in the FASTA header #103
2020-08-28qc_fasta returns also the seq_type; verified that only one FASTA is sent at ↵AndreaGuarracino
a time; code cleaning
2020-08-28fixed local QC, modifying the regex for FASTA/FASTQ to be more generalAndreaGuarracino
2020-08-27updated dependency from clustalw to minimap2; the genbank script no longer ↵AndreaGuarracino
creates YAML/FASTA pairs for too short sequences
2020-08-26Increase RAM for odgi-build-from-spoa-gfaPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-08-26updated parameter nameAndreaGuarracino
2020-08-26added option in the genbank script to ignore (already validated) IDs; code ↵AndreaGuarracino
cleaning; typos
2020-08-26typos in the code; little code refactoringAndreaGuarracino
2020-08-26DocsPjotr Prins
2020-08-26Fix underscoresPjotr Prins
2020-08-25Increase RAM requirement for sort_fasta_by_quality_and_lenPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-08-25Using ArvadosPjotr Prins
2020-08-25the YAML/FASTA pair is not created for samples where at least one mandatory ↵AndreaGuarracino
field is missing
2020-08-24fixed protocol for the dictionary entries that caused validation problemsAndreaGuarracino
2020-08-24Fix dependency conflict with PyShExCPeter Amstutz
2020-08-24Adding meta keywords to HTMLPjotr Prins
2020-08-24genbank script documented in blogPjotr Prins
2020-08-24reverted the relaxation on the location attributeAndreaGuarracino
2020-08-24Merge pull request #102 from AndreaGuarracino/patch-4Pjotr Prins
a lot of new ontology terms, genbank/sra scripts updated to be more general
2020-08-24Genbank uploadPjotr Prins
2020-08-24Add note on most fields being optionalPjotr Prins
2020-08-24ImagesPjotr Prins
2020-08-23More infoPjotr Prins
2020-08-23Textual changesPjotr Prins
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
2020-08-22GeneratedPjotr Prins
2020-08-22Relaxing the location attributePjotr Prins
2020-08-22FASTQ in capitalsPjotr Prins
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