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
2020-07-07
Merge pull request #90 from AndreaGuarracino/patch-21
LLTommy
2020-07-07
fix missing authors #91
AndreaGuarracino
2020-07-07
minimap2 returns nothing when there is no alignment.
Peter Amstutz
2020-07-07
if the technology is not found, the YAML file is not created; managed longer ...
AndreaGuarracino
2020-07-06
renamed sra script; added seq technology in its additional information field ...
AndreaGuarracino
2020-07-06
fix ncbi_countries dictionary
AndreaGuarracino
2020-07-06
new terms in the ncbi_countries dictionary
Andrea Guarracino
2020-07-06
added seq technology in its additional information field if the term is missi...
AndreaGuarracino
2020-07-06
updated SraExperimentPackage info
AndreaGuarracino
2020-07-06
two more terms in the ncbi_sequencing_technology dictionary
Andrea Guarracino
2020-07-06
fixed bugs in the download_sra_data
Andrea Guarracino
2020-07-06
new terms in the sequencing_technology dictionary
Andrea Guarracino
2020-07-03
Add upload.cwl
Peter Amstutz
2020-07-03
Improving genbank import workflow
Peter Amstutz
2020-06-22
very little readme for the scripts
Andrea Guarracino
2020-06-22
added new script to prepare metadata of sra data
AndreaGuarracino
2020-06-22
moved the genbank script in his specific directory
AndreaGuarracino
2020-06-22
added new dictionary entries
AndreaGuarracino
2020-06-22
little fix for specimen_source
Andrea Guarracino
2020-06-22
new entries for the EBI samples
AndreaGuarracino
2020-06-22
corrected the wrong entities
Andrea Guarracino
2020-06-22
Handle upload & assembly of gzipped, paired-end fastq
Peter Amstutz
2020-06-15
virtuoso: remove graph before update
Pjotr Prins
2020-06-12
species dictionary
Andrea Guarracino
2020-06-12
species are managed in another dictionary, try-catch added to avoid unexpecte...
Andrea Guarracino
2020-06-07
the script is more verbose; added other countries
AndreaGuarracino
2020-06-06
fixed collection_location when it is not present in the dictionary terms
AndreaGuarracino
2020-06-06
fixed collection-date management using a parser
AndreaGuarracino
2020-06-06
fixed collection-date management; updated assembly info management for new IDs
AndreaGuarracino
2020-05-31
Added new speciesman sources
Andrea Guarracino
2020-05-31
Added new sequencing technologies
Andrea Guarracino
2020-05-31
Added new countries
Andrea Guarracino
2020-05-31
Added new species and specimen sources
Andrea Guarracino
2020-05-31
Updated the host_sex and host_age management
Andrea Guarracino
2020-05-31
The NCBI Virus entries are updated automatically
Andrea Guarracino
2020-05-20
Virtuoso update in CRON
Pjotr Prins
2020-05-13
Virtuoso uploader: always upload countries and labels
Pjotr Prins
2020-05-13
Virtuoso: split named graphs
Pjotr Prins
2020-05-12
Virtuoso uploader: does not delete graph yet
Pjotr Prins
2020-05-12
Update graph script
Pjotr Prins
2020-04-30
fixed UO_0000036 for year
Andrea Guarracino
2020-04-30
Merge pull request #41 from AndreaGuarracino/patch-14
LLTommy
2020-04-30
Import script fixes
Peter Amstutz
2020-04-30
Wrap import script to run as a workflow
Peter Amstutz
2020-04-29
the date is now handled more formally
Andrea Guarracino
2020-04-29
Reverting country list back, something went wrong there
lltommy
2020-04-28
updated to manage list fields and added new control on nasopharyngeal/throat ...
Andrea Guarracino
2020-04-28
Updated with new terms
Andrea Guarracino
2020-04-28
Updated with new terms
Andrea Guarracino
2020-04-28
Updated - 1731 IDs - 2020/04/28
Andrea Guarracino
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