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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.
2020-07-03Add --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
2020-07-03Fix single arg uploadPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-06-22Better invalid sequence QC handlingPeter Amstutz
2020-06-22Handle upload & assembly of gzipped, paired-end fastqPeter Amstutz
2020-05-29Changed doc comment in schemaPjotr Prins
2020-05-29Improved error output for the web uploaderPjotr Prins
2020-05-28Web: debugging metadata submissionPjotr Prins
2020-05-28Uploader: validate metadata first (it is faster)Pjotr Prins
2020-05-06Adding additional frontend option (PATO_0001340) to QClltommy
2020-04-30Handle running in a container with no usernamePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Last addition/edits to the meta data schemalltommy
2020-04-29Use subprocess invocation is backwards compatible with Python 3.5Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29Add referencePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-28Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-28Decision to settle for float instead of integers for the coveragelltommy
2020-04-28Call clustalw to compare sequence to referencePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-28Changes to the structure - we use lists now instead of strings where it ↵lltommy
makes sense. This allows us to have multiple values where in makes sense
2020-04-23adding a submitter comment fieldlltommy
2020-04-23Adding a third sequence technology optionlltommy
2020-04-23Merge branch 'master' into patch-3LLTommy
2020-04-22Fixing ShEx expression, one ? too muchlltommy
2020-04-22Forgot to add _idlltommy
2020-04-22Including restrictions to the host statuslltommy
2020-04-22Small changes all around, trying to make the importer/metadata betterlltommy
2020-04-21Work around CWL content size limit by chunkingPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21add noLinkCheck to specimen_source2Peter Amstutz
2020-04-21Tweak handling of "coverage" also fix typoPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Working on NCBI importPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Updated shex and manditory fields and stufflltommy
2020-04-20Reconsidered these should be noLinkCheckPeter Amstutz
2020-04-20Add identity:true to collection_locationPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Schema changes from @LLTommyPeter Amstutz
2020-04-20Better handling of duplicate sequencesPeter Amstutz
Also save original fasta label in metadata
2020-04-20Make doc not contradict option listAdam Novak
2020-04-20Put back Intersex with the closest PATO equivalentAdam Novak
These options still disagree with the doc string in the schema.
2020-04-20Add ShEx validationPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Making collection date and collection location MANDATORY fields, turning ↵lltommy
orcid into IRI
2020-04-20Fixing string -> URI in speciman, plus other thingslltommy
2020-04-19small updates to the yaml schema, updating the example fileslltommy
2020-04-19Updating NCBI dictonaries, adding UI options, small yaml schema changeslltommy
2020-04-19Merge pull request #24 from adamnovak/dropdownsPjotr Prins
Add dropdown support to web uploader metadata form
2020-04-18Extending yaml schema a bit and adding additional information for the UIlltommy
2020-04-17Copy NCIT IRIs back to schema docAdam Novak
2020-04-17Spruce up the options file and add missing valuesAdam Novak
2020-04-17Create option dropdowns from an options fileAdam Novak
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