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
about
summary
refs
log
tree
commit
diff
log msg
author
committer
range
path:
root
/
workflows
Age
Commit message (
Expand
)
Author
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
2020-05-05
preserve the directory layout of segmentation.py
Michael R. Crusoe
2020-05-05
move some tools into the shared repo
Michael R. Crusoe
2020-05-04
bump jerven/spodgi image to 0.0.6
Peter Amstutz
2020-05-04
add pangenome browser prep
Michael R. Crusoe
2020-05-04
Increase RAM for minimap2
Peter Amstutz
2020-05-03
Set a RAM requirement on odgi_to_rdf to influence it to run on c5
Peter Amstutz
2020-05-01
Set verison tag on spodgi container image
Peter Amstutz
2020-04-28
Update spodgi docker image
Peter Amstutz
2020-04-21
Increase ram requirement for minimap2
Peter Amstutz
2020-04-21
Workaround CWL limit by chunking file list
Peter Amstutz
2020-04-21
Work around CWL content size limit by chunking
Peter Amstutz
2020-04-20
Add readsMergeDedup.fasta to output
Peter Amstutz
2020-04-20
Make sure there is a newline in relabeled fasta (but no blank lines)
Peter Amstutz
2020-04-20
Better handling of duplicate sequences
Peter Amstutz
2020-04-20
Relabel sequences to match metadata subjects.
Peter Amstutz
2020-04-20
Move workflows into main repo
Peter Amstutz