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2020-07-07minimap2 returns nothing when there is no alignment.Peter Amstutz
2020-07-07Use minimap2 instead of clustalw for fasta QCPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-05Add 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>
2020-06-25Update 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
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
2020-06-22Adjust QC filter and relabel output sequence with sample_idPeter Amstutz
2020-06-22Merge pull request #86 from AndreaGuarracino/patch-19Peter Amstutz
corrected the wrong entities
2020-06-22new entries for the EBI samplesAndreaGuarracino
2020-06-22Better invalid sequence QC handlingPeter Amstutz
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
2020-06-18removed double sortingAndrea Guarracino
The -s argument in odgi build do the same thing that odgi sort -p s does.
2020-06-18Merge pull request #84 from BonfaceKilz/masterPjotr Prins
fix: show missing markers
2020-06-18fix(map): update fasta count keyBonfaceKilz
2020-06-18fix: show missing markersBonfaceKilz
The SPARQL query returns "-85.58 44.34" instead of "Point(-85.58 44.34)", so the markers could not be displayed
2020-06-17Slighlty alter SPARQL query to truley sumarize locations for contients. Most ↵lltommy
likley this number must be combined with what is assigned directly to a country? (instead of e.g.) a city?
2020-06-17Merge pull request #83 from BonfaceKilz/feature/display-content-sequencesLLTommy
Feature/display fasta count on a map
2020-06-17Add cluster marker groupBonfaceKilz
When markers are close together, lump them together. Also, it provides a convenient method of remove markers when loading other GPS co-ordinates
2020-06-17Move map logic to main.jsBonfaceKilz
2020-06-17Move js script to bottom of pageBonfaceKilz
Methods associated with map need to be created after the div container
2020-06-17Add styling to mapBonfaceKilz
2020-06-17Fix broken HTMLBonfaceKilz
2020-06-17Move leaflet CSS to the head sectionBonfaceKilz
2020-06-17Add section for map and add basic stylingBonfaceKilz
2020-06-17Add leaflet css and js libsBonfaceKilz
2020-06-17Remove literal json representation of mapBonfaceKilz
2020-06-16starting to include a maplltommy
2020-06-15Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-06-15Adding endpoints using grouping of continentslltommy
2020-06-15virtuoso: remove graph before updatePjotr Prins
2020-06-14Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-06-14Tried to make a start with the 'demo' part, table works, drilling down notlltommy
2020-06-12Merge pull request #82 from AndreaGuarracino/patch-17LLTommy
the script is more robust and verbose
2020-06-12Adding endpoint getCountByGPS which could be used to draw a maplltommy
2020-06-12species dictionaryAndrea Guarracino
2020-06-12species are managed in another dictionary, try-catch added to avoid ↵Andrea Guarracino
unexpected stops
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