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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Author
2020-10-28
Adding more metadata to resource uri
Pjotr Prins
2020-10-28
Create permalink and some output
Pjotr Prins
2020-10-28
Use Flask url_for to make relative routes work
Pjotr Prins
2020-10-28
Fix CSS errors
Pjotr Prins
2020-10-27
Commented in uploader main.py
Pjotr Prins
2020-10-27
Updating docs
Pjotr Prins
2020-10-26
Update blog
Pjotr Prins
2020-10-26
Minor CSS for the map
Pjotr Prins
2020-10-26
Improved map to show sequences in one view
Pjotr Prins
2020-10-26
Adding upload metadata examples
Pjotr Prins
2020-10-26
Textual updates
Pjotr Prins
2020-10-06
Create .dockstore.yml
Michael R. Crusoe
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
2020-09-29
esr_samples script refactoring; added a reference of the esr_samples script i...
AndreaGuarracino
2020-09-28
new countries; updated genbank/sra scripts to manage more specimen sources
AndreaGuarracino
2020-09-28
genbank and sra scripts more picky on the ontologies; added utils.py for shar...
AndreaGuarracino
2020-09-27
Virtuoso uploader: instructions
Pjotr Prins
2020-09-27
Virtuoso uploader: explicit output
Pjotr Prins
2020-09-27
Fixing missing dot in .ttl file
lltommy
2020-09-27
Adding script supporting semantic enrichment
lltommy
2020-09-27
Adding a few labels to other used vocabs
lltommy
2020-09-27
Updated country labels and GPS coordinates
lltommy
2020-09-26
script for processing the metadata of the ESR samples; moved delete_entries_o...
AndreaGuarracino
2020-09-25
added new New Zealand entries
AndreaGuarracino
2020-09-05
increased the quality filter threshold
AndreaGuarracino
2020-09-04
fixed bugs in in index management and type conversion
AndreaGuarracino
2020-09-04
sra script re-enabled, ready for tests
AndreaGuarracino
2020-09-04
added in the sra script an option to include only a subset of ids
AndreaGuarracino
2020-09-04
sra script updated for managing more locations
AndreaGuarracino
2020-09-04
synchronized the create_sra_metadata.py script with the latest updates
AndreaGuarracino
2020-08-29
fixed few countries ontology terms; added a new species
AndreaGuarracino
2020-08-28
added script to remove entries on Arvados
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
2020-08-27
updated dependency from clustalw to minimap2; the genbank script no longer cr...
AndreaGuarracino
2020-08-26
Increase RAM for odgi-build-from-spoa-gfa
Peter Amstutz
2020-08-26
updated parameter name
AndreaGuarracino
2020-08-26
added option in the genbank script to ignore (already validated) IDs; code cl...
AndreaGuarracino
2020-08-26
typos in the code; little code refactoring
AndreaGuarracino
2020-08-26
Docs
Pjotr Prins
2020-08-26
Fix underscores
Pjotr Prins
2020-08-25
Increase RAM requirement for sort_fasta_by_quality_and_len
Peter Amstutz
2020-08-25
Using Arvados
Pjotr Prins
2020-08-25
the YAML/FASTA pair is not created for samples where at least one mandatory f...
AndreaGuarracino
2020-08-24
fixed protocol for the dictionary entries that caused validation problems
AndreaGuarracino
2020-08-24
Fix dependency conflict with PyShExC
Peter Amstutz
2020-08-24
Adding meta keywords to HTML
Pjotr Prins
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