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
2020-07-05
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
2020-05-29
Improved error output for the web uploader
Pjotr Prins
2020-05-28
Web: debugging metadata submission
Pjotr Prins
2020-05-28
Uploader: validate metadata first (it is faster)
Pjotr Prins
2020-05-06
Adding additional frontend option (PATO_0001340) to QC
lltommy
2020-04-30
Handle running in a container with no username
Peter Amstutz
2020-04-30
Last addition/edits to the meta data schema
lltommy
2020-04-29
Use subprocess invocation is backwards compatible with Python 3.5
Peter Amstutz
2020-04-29
Add reference
Peter Amstutz
2020-04-28
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
lltommy
2020-04-28
Decision to settle for float instead of integers for the coverage
lltommy
2020-04-28
Call clustalw to compare sequence to reference
Peter Amstutz
2020-04-28
Changes to the structure - we use lists now instead of strings where it makes...
lltommy
2020-04-23
adding a submitter comment field
lltommy
2020-04-23
Adding a third sequence technology option
lltommy
2020-04-23
Merge branch 'master' into patch-3
LLTommy
2020-04-22
Fixing ShEx expression, one ? too much
lltommy
2020-04-22
Forgot to add _id
lltommy
2020-04-22
Including restrictions to the host status
lltommy
2020-04-22
Small changes all around, trying to make the importer/metadata better
lltommy
2020-04-21
Work around CWL content size limit by chunking
Peter Amstutz
2020-04-21
add noLinkCheck to specimen_source2
Peter Amstutz
2020-04-21
Tweak handling of "coverage" also fix typo
Peter Amstutz
2020-04-21
Working on NCBI import
Peter Amstutz
2020-04-21
Updated shex and manditory fields and stuff
lltommy
2020-04-20
Reconsidered these should be noLinkCheck
Peter Amstutz
2020-04-20
Add identity:true to collection_location
Peter Amstutz
2020-04-20
Schema changes from @LLTommy
Peter Amstutz
2020-04-20
Better handling of duplicate sequences
Peter Amstutz
2020-04-20
Make doc not contradict option list
Adam Novak
2020-04-20
Put back Intersex with the closest PATO equivalent
Adam Novak
2020-04-20
Add ShEx validation
Peter Amstutz
2020-04-20
Making collection date and collection location MANDATORY fields, turning orci...
lltommy
2020-04-20
Fixing string -> URI in speciman, plus other things
lltommy
2020-04-19
small updates to the yaml schema, updating the example files
lltommy
2020-04-19
Updating NCBI dictonaries, adding UI options, small yaml schema changes
lltommy
2020-04-19
Merge pull request #24 from adamnovak/dropdowns
Pjotr Prins
2020-04-18
Extending yaml schema a bit and adding additional information for the UI
lltommy
2020-04-17
Copy NCIT IRIs back to schema doc
Adam Novak
2020-04-17
Spruce up the options file and add missing values
Adam Novak
2020-04-17
Create option dropdowns from an options file
Adam Novak
2020-04-15
Typo: submitter_orchid -> submitter_orcid
Stian Soiland-Reyes
2020-04-15
Changing vaccination URI
lltommy
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