index
:
bh20-seq-resource
analysis-refactor
fasta-subset-from-query
generate-cwl
master
new_assembly_method_field
pangenome_workflow_abpoa
upload-download-status
uuid-for-resource
yamlfa2ttl
Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis
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bh20sequploader
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Author
2020-11-13
there can be two specimen terms
AndreaGuarracino
2020-11-13
Yaml and ShEx changes
lltommy
2020-11-12
added closed shapes
AndreaGuarracino
2020-11-12
added missing _type: "@id" to the assembly_method field in the schema
AndreaGuarracino
2020-11-12
Trying to fix the submitter shape, shex and yaml
lltommy
2020-11-12
Proposed new technology shape/yaml structure
lltommy
2020-11-11
Support uploading new metadata only
Peter Amstutz
2020-11-11
Documenting and QC of YAML. Some conflicts discovered that need review
lltommy
2020-11-11
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
lltommy
2020-11-11
restricting specimen_source to obo:NCIT which would have prevented the ncbi t...
lltommy
2020-11-07
RDF: use URIs
Pjotr Prins
2020-11-07
Fixed the License error (https!!)
Pjotr Prins
2020-11-06
Uploader script improvements
Pjotr Prins
2020-11-04
fixed sequence_assembly_method field description
AndreaGuarracino
2020-10-27
Commented in uploader main.py
Pjotr Prins
2020-10-01
sequence divergence to 5% for minimap2 in the FASTA quality control
AndreaGuarracino
2020-10-01
show more information in the error messages
AndreaGuarracino
2020-09-04
fixed bugs in in index management and type conversion
AndreaGuarracino
2020-08-28
local QC is optional
AndreaGuarracino
2020-08-28
added control (locally and in the validation) that sample_id has to be the sa...
AndreaGuarracino
2020-08-28
qc_fasta returns also the seq_type; verified that only one FASTA is sent at a...
AndreaGuarracino
2020-08-28
fixed local QC, modifying the regex for FASTA/FASTQ to be more general
AndreaGuarracino
2020-08-26
updated parameter name
AndreaGuarracino
2020-08-26
typos in the code; little code refactoring
AndreaGuarracino
2020-08-24
reverted the relaxation on the location attribute
AndreaGuarracino
2020-08-22
Relaxing the location attribute
Pjotr Prins
2020-07-16
Report similarity == 0
Peter Amstutz
2020-07-16
Improve uploader reporting.
Peter Amstutz
2020-07-16
Make license optional
Peter Amstutz
2020-07-16
Make license optional for now
Peter Amstutz
2020-07-16
Make license optional for now
Pjotr Prins
2020-07-15
License RDF
Pjotr Prins
2020-07-15
Add RDF output
Pjotr Prins
2020-07-15
Web: add license to input form
Pjotr Prins
2020-07-13
Add ontology and schema for license information. For review.
Pjotr Prins
2020-07-08
Try to fix lab_address wrong predicate, fix submitter shape on the way and ho...
lltommy
2020-07-08
Give uploader an option to trust local validation (for batch imports)
upload-download-status
Peter Amstutz
2020-07-08
Uploader checks for duplicates
Peter Amstutz
2020-07-08
Avoid redundant loading of schema
Peter Amstutz
2020-07-08
Hack in a valid-uri check
Peter Amstutz
2020-07-07
minimap2 returns nothing when there is no alignment.
Peter Amstutz
2020-07-07
Use minimap2 instead of clustalw for fasta QC
Peter Amstutz
2020-07-05
Add bh20-seq-analyzer --print-status
Peter Amstutz
2020-07-03
Add --skip-qc for faster batch import
Peter Amstutz
2020-07-03
Adding --skip-qc
Peter Amstutz
2020-07-03
Fix qc_fasta bug closing stream.
Peter Amstutz
2020-07-03
Fix single arg upload
Peter Amstutz
2020-06-22
Better invalid sequence QC handling
Peter Amstutz
2020-06-22
Handle upload & assembly of gzipped, paired-end fastq
Peter Amstutz
2020-05-29
Changed doc comment in schema
Pjotr Prins
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