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
2020-07-17
Comment out some broken links for now
Peter Amstutz
2020-07-17
Preparing for EBI submission
Pjotr Prins
2020-07-17
Started EBI submission
Pjotr Prins
2020-07-16
Report similarity == 0
Peter Amstutz
2020-07-16
Cleanup script also clears errors for revalidate
Peter Amstutz
2020-07-16
Catch exceptions
Peter Amstutz
2020-07-12
added a suffix to distinguish which script created the error/warning files
AndreaGuarracino
2020-07-10
metadata with missing host_species are not created
AndreaGuarracino
2020-07-10
an output file is created with the accessions for which no YAML file is created
AndreaGuarracino
2020-07-10
updated metadata source
AndreaGuarracino
2020-07-10
other term for Homo sapiens (for SRA samples)
Andrea Guarracino
2020-07-09
fixed bug that lead to invalid sample_sequencing_technology values
Andrea Guarracino
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
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