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2020-04-10Propagating metadata to output works now.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-10Improve fasta/fastq QCPeter Amstutz
2020-04-10Fix swapped fasta/fastqPeter Amstutz
Replace example sequence with COV19 reference instead of HIV. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-10Add qc_fastaPeter Amstutz
2020-04-10Fix up fasta/fastq validationPeter Amstutz
2020-04-10Validate & propagate metadataPeter Amstutz
2020-04-10Magic dependencyPjotr Prins
2020-04-10Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-04-10Merge pull request #6 from uniqueg/fa_fq_validationPjotr Prins
validate seq format with magic file
2020-04-10Note on running container with GuixPjotr Prins
2020-04-10This fixedPjotr Prins
{'type': 'string?', 'jsonldPredicate': {'_id': 'http://purl.obolibrary.org/obo/UO_0000036'}} {'type': 'string?', 'jsonldPredicate': 'http://purl.obolibrary.org/obo/NCIT_C25688'} Traceback (most recent call last): (...) File "/export/iwrk/opensource/code/vg/bh20-seq-resource/bh20simplewebuploader/main.py", line 106, in walk_fields for item in walk_fields(field_type, parent_keys + [field_name], subtree_optional or optional): File "/export/iwrk/opensource/code/vg/bh20-seq-resource/bh20simplewebuploader/main.py", line 92, in walk_fields ref_url = field_type.get('jsonldPredicate', {}).get('_id', None) AttributeError: 'str' object has no attribute 'get'
2020-04-10Fixed TypeError: 'module' object is not callablePjotr Prins
2020-04-10Cleaned up Guix install instructionsPjotr Prins
2020-04-10validate seq format with magic fileAlex Kanitz
2020-04-10Updating schema and examples, including URIslltommy
2020-04-10Merge pull request #4 from adamnovak/add-web-uiPjotr Prins
Add Web UI
2020-04-10Merge pull request #3 from adamnovak/patch-1Pjotr Prins
Spell correctly
2020-04-09Move the web uploader GUIX instructions to the GUIX fileAdam Novak
2020-04-09Point to new repo for sourceAdam Novak
2020-04-09Merge remote-tracking branch 'upstream/master' into add-web-uiAdam Novak
2020-04-09Copy over/combine top-level project componentsAdam Novak
2020-04-09Merge branch 'move-repo' of ../bh20-simple-web-uploader into HEADAdam Novak
2020-04-09Put back in directoryAdam Novak
2020-04-09NotesPjotr Prins
2020-04-09Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-04-09Moved Guix documentation into separate file (as it confused people ;)Pjotr Prins
2020-04-09Propagate metadata to pangenome so it can be merged by workflowPeter Amstutz
2020-04-09Spacing and typoPjotr Prins
2020-04-09Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-04-09Add "sequencefile" for the metadata subject.Peter Amstutz
2020-04-09Make schema link nicer and add example filesAdam Novak
2020-04-09Don't include pycAdam Novak
2020-04-09Add auto-generated fillable metadata formAdam Novak
2020-04-09Adding functionality of turning keys into ontology terms (URI). This is work ↵lltommy
in progress - of course!
2020-04-09Updating schema and examples. This is still work in progress but we get therelltommy
2020-04-08Add context linksAdam Novak
2020-04-08Don't assert that the metadata is really JSON-LDAdam Novak
2020-04-08Fastq now runs through fastq2fasta pipelinePeter Amstutz
then gets added to pangenome analysis.
2020-04-08Initial commit of working frontendAdam Novak
2020-04-08Spell correctlyAdam Novak
2020-04-08titlePjotr Prins
2020-04-08PaperPjotr Prins
2020-04-07Merge pull request #2 from adamnovak/instructionsPeter Amstutz
Make README more didactic
2020-04-07Add metadata validation with schema-saladPeter Amstutz
2020-04-07Make README more didacticAdam Novak
2020-04-07limit 1Peter Amstutz
2020-04-07Copy recent results to a set destinationPeter Amstutz
2020-04-07Note on upload-resumePjotr Prins
2020-04-07Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-07adding dummy metadata qc to the projectlltommy
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