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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
2020-07-09Skip certificate check - this was upstreamed in Arvados, so we can remove laterPjotr Prins
2020-07-09Merge pull request #93 from AndreaGuarracino/patch-22Pjotr Prins
fixed bug that lead to invalid sample_sequencing_technology values
2020-07-09fixed bug that lead to invalid sample_sequencing_technology valuesAndrea Guarracino
2020-07-08Adding missing GPS coordinates et alllltommy
2020-07-08Try to fix lab_address wrong predicate, fix submitter shape on the way and ↵lltommy
hopefully brought it in synch with the yaml
2020-07-08Merge pull request #92 from arvados/upload-download-statusPeter Amstutz
Split upload tab. Add upload status tab. Also a bunch of QC and uploader improvements.
2020-07-08Give uploader an option to trust local validation (for batch imports)upload-download-statusPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-08Uploader checks for duplicatesPeter Amstutz
2020-07-08Avoid redundant loading of schemaPeter Amstutz
2020-07-08Add --revalidate and fix checking/updating properties.Peter Amstutz
2020-07-08Hack in a valid-uri checkPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-08Get count from arvadosPeter Amstutz
Separate pending/rejected tables "Lastest results" is latest successful run. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-08Fetch status as anonymous userPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-08Split upload tab. Add upload status tab.Peter Amstutz
Add more direct links on download page. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-08Merge pull request #89 from proccaserra/patch-1LLTommy
Update form.html
2020-07-07Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-07-07Adding some more country labels. Some GPS are still missing, will handle in ↵lltommy
the future
2020-07-07Adding sequencer labelslltommy
2020-07-07Merge pull request #90 from AndreaGuarracino/patch-21LLTommy
genbank and sra scripts update, new terms in the ontology dictionaries
2020-07-07--print-status=html creates html reportPeter Amstutz
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
2020-07-07Use minimap2 instead of clustalw for fasta QCPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
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
2020-07-05Add bh20-seq-analyzer --print-statusPeter Amstutz
Get status from new property "status: validated/rejected" Also store QC fail error message.
2020-07-03A little more loggingPeter Amstutz
2020-07-03Add upload.cwlPeter Amstutz
2020-07-03Add --no-start-analysisPeter Amstutz
2020-07-03Add --skip-qc for faster batch importPeter Amstutz
2020-07-03Adding --skip-qcPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-03Fix qc_fasta bug closing stream.Peter Amstutz
2020-07-03Improving genbank import workflowPeter Amstutz
2020-07-03Fix single arg uploadPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-03Update form.htmlPhilippe Rocca-Serra
s/onthology/ontology/
2020-06-25Update labels.ttlLLTommy
adding label for "Illumina HiSeq X"
2020-06-24Merge pull request #87 from AndreaGuarracino/patch-20LLTommy
added script to crete metadata for SRA data; new dictionary entries; little directory changes
2020-06-24Merge pull request #85 from AndreaGuarracino/patch-18LLTommy
removed double sorting
2020-06-22very little readme for the scriptsAndrea Guarracino
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