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
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
2020-11-10
Use arvados uuids for RDF subjects.
uuid-for-resource
Peter Amstutz
2020-11-09
Make resource link work for both portable data hashes and sample id
Peter Amstutz
2020-11-09
Make it so "pangenome analysis" only runs collect-seqs.
Peter Amstutz
2020-11-09
Rename schema param to metadataSchema
Peter Amstutz
2020-11-09
Extract subset of the all-sequences fasta by running a sparql query.
Peter Amstutz
2020-09-26
script for processing the metadata of the ESR samples; moved delete_entries_o...
AndreaGuarracino
2020-09-05
increased the quality filter threshold
AndreaGuarracino
2020-08-28
added script to remove entries on Arvados
AndreaGuarracino
2020-08-26
Increase RAM for odgi-build-from-spoa-gfa
Peter Amstutz
2020-08-25
Increase RAM requirement for sort_fasta_by_quality_and_len
Peter Amstutz
2020-08-19
Fix output parameters
Peter Amstutz
2020-08-19
Scaling pangenome generation
Peter Amstutz
2020-08-19
Consolidate steps to scale graph generation workflow
Peter Amstutz
2020-08-19
used builtin hashlib md5 for the deduplication step
AndreaGuarracino
2020-08-19
integrated the deduplication step in the sorting by quality and length script
AndreaGuarracino
2020-07-27
added workflow to sort a multifasta by quality and length, and added the over...
AndreaGuarracino
2020-07-27
added spoa workflow in a low memory consumption mode
AndreaGuarracino
2020-07-27
new workflow for odgi building from spoa gfa
AndreaGuarracino
2020-06-24
Merge pull request #85 from AndreaGuarracino/patch-18
LLTommy
2020-06-22
Adjust QC filter and relabel output sequence with sample_id
Peter Amstutz
2020-06-18
removed double sorting
Andrea Guarracino
2020-06-11
tweaks for proper graph browser output
Michael R. Crusoe
2020-06-02
update tool sub repo
Michael R. Crusoe
2020-05-26
Can have list of sequence labels to exclude from combined fasta
Peter Amstutz
2020-05-14
Workflow fixes
Peter Amstutz
2020-05-11
Merge pull request #49 from mr-c/add_pangenome_browser_prep
Peter Amstutz
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