Age | Commit message (Collapse) | Author | |
---|---|---|---|
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 sequencespangenome_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 | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-11-18 | Fix typo. Give from_sparql more RAM. | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-11-18 | Add query-to-gfa workflow | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-11-11 | Make collect-seqs skip bad inputs. | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-11-10 | Use arvados uuids for RDF subjects.uuid-for-resource | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-11-09 | Make resource link work for both portable data hashes and sample id | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-11-09 | Make it so "pangenome analysis" only runs collect-seqs. | Peter Amstutz | |
Will ensure that metadata is kept up to date. GFA isn't being generated. Will introduce new workflow that uses from_sparql to analyze a subset. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-11-09 | Rename schema param to metadataSchema | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-11-09 | Extract subset of the all-sequences fasta by running a sparql query. | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-09-26 | script for processing the metadata of the ESR samples; moved ↵ | AndreaGuarracino | |
delete_entries_on_arvados script in scripts directory | |||
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 | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-25 | Increase RAM requirement for sort_fasta_by_quality_and_len | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-19 | Fix output parameters | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-19 | Scaling pangenome generation | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-08-19 | Consolidate steps to scale graph generation workflow | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
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 ↵ | AndreaGuarracino | |
overall new pangenome generation workflow with SPOA | |||
2020-07-27 | added spoa workflow in a low memory consumption mode | AndreaGuarracino | |