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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2021-01-07
Allow for xml and xml.gz files
Pjotr Prins
2021-01-06
cleaned utils.py
AndreaGuarracino
2021-01-06
Pubseq fetch: sometimes a request times out. So repeat with intervals.
Pjotr Prins
2021-01-05
cleaning update-from-genbank.py; removed unused import from genbank-fetch-ids.py
AndreaGuarracino
2021-01-05
cleaning genbank-fetch-ids.py
AndreaGuarracino
2021-01-05
Fetching fixes
Pjotr Prins
2021-01-05
Add option for fetching fasta
Pjotr Prins
2021-01-05
fetch: do a straight dump of the original record
Pjotr Prins
2021-01-05
fetches original metadata from PubSeq/Arvados
Pjotr Prins
2021-01-05
API: fix returned record to include original metadata
Pjotr Prins
2021-01-05
Rename
Pjotr Prins
2021-01-04
mapping: no longer requires specimen file for genbank output
Pjotr Prins
2021-01-04
Removing refs. No point in guessing terms
Pjotr Prins
2021-01-04
mapping sample_species using regex
Pjotr Prins
2021-01-04
Started on normalization
Pjotr Prins
2021-01-03
genbank: specimen source
Pjotr Prins
2021-01-03
genbank: more or less complete. Need to add collection method
Pjotr Prins
2021-01-03
genbank: deal with host, sex and age
Pjotr Prins
2021-01-03
genbank: technology parsing
Pjotr Prins
2021-01-03
genbank: submitter info
Pjotr Prins
2021-01-03
genbank: get authors
Pjotr Prins
2021-01-03
Move reference code to different file so it does not break python
Pjotr Prins
2021-01-02
GenBank date parsing
Pjotr Prins
2021-01-02
transform-genbank-xml2yamlfa.py refactoring
Pjotr Prins
2021-01-02
transform-genbank-xml2yamlfa.py rewrite
Pjotr Prins
2021-01-01
genbank: minor fixes
Pjotr Prins
2021-01-01
gzip output
Pjotr Prins
2021-01-01
update-from-genbank.py
Pjotr Prins
2021-01-01
genbank-fetch-ids.py
Pjotr Prins
2021-01-01
genbank-fetch-ids
Pjotr Prins
2021-01-01
genbank: cleaning up
Pjotr Prins
2021-01-01
genbank-fetch-ids simple call
Pjotr Prins
2021-01-01
sparql: make use of pattern matching
Pjotr Prins
2020-12-31
Add comment
Pjotr Prins
2020-12-31
Improve SPARQL query and comments
Pjotr Prins
2020-12-31
genbank: sparql-fetch-ids
Pjotr Prins
2020-12-31
sparql: rename file
Pjotr Prins
2020-12-31
genbank: started on SPARQL fetcher
Pjotr Prins
2020-12-31
genbank: pseudo workflow
Pjotr Prins
2020-12-31
genbank: header
Pjotr Prins
2020-12-31
genbank: split script
Pjotr Prins
2020-12-31
genbank: moving script into workflow space
Pjotr Prins
2020-11-21
abPOA works better starting from shorter sequences
pangenome_workflow_abpoa
AndreaGuarracino
2020-11-21
added abPOA workflow; typos
AndreaGuarracino
2020-11-21
added reversed_sorting parameter; typos
AndreaGuarracino
2020-11-21
generalized spoa workflow
AndreaGuarracino
2020-11-18
Give from_sparql more keep cache.
Peter Amstutz
2020-11-18
Fix typo. Give from_sparql more RAM.
Peter Amstutz
2020-11-18
Add query-to-gfa workflow
Peter Amstutz
2020-11-11
Make collect-seqs skip bad inputs.
Peter Amstutz
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