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2020-11-21abPOA works better starting from shorter sequencespangenome_workflow_abpoaAndreaGuarracino
2020-11-21added abPOA workflow; typosAndreaGuarracino
2020-11-21added reversed_sorting parameter; typosAndreaGuarracino
2020-11-21generalized spoa workflowAndreaGuarracino
2020-11-18Give from_sparql more keep cache.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-18Fix typo. Give from_sparql more RAM.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-18Add query-to-gfa workflowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-11Make collect-seqs skip bad inputs.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-10Use arvados uuids for RDF subjects.uuid-for-resourcePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-09Make resource link work for both portable data hashes and sample idPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-09Make 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>
2020-11-09Rename schema param to metadataSchemaPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-09Extract 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>
2020-09-26script for processing the metadata of the ESR samples; moved ↵AndreaGuarracino
delete_entries_on_arvados script in scripts directory
2020-09-05increased the quality filter thresholdAndreaGuarracino
2020-08-28added script to remove entries on ArvadosAndreaGuarracino
2020-08-26Increase RAM for odgi-build-from-spoa-gfaPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-08-25Increase RAM requirement for sort_fasta_by_quality_and_lenPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-08-19Fix output parametersPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-08-19Scaling pangenome generationPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-08-19Consolidate steps to scale graph generation workflowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-08-19used builtin hashlib md5 for the deduplication stepAndreaGuarracino
2020-08-19integrated the deduplication step in the sorting by quality and length scriptAndreaGuarracino
2020-07-27added workflow to sort a multifasta by quality and length, and added the ↵AndreaGuarracino
overall new pangenome generation workflow with SPOA
2020-07-27added spoa workflow in a low memory consumption modeAndreaGuarracino
2020-07-27new workflow for odgi building from spoa gfaAndreaGuarracino
2020-06-24Merge pull request #85 from AndreaGuarracino/patch-18LLTommy
removed double sorting
2020-06-22Adjust QC filter and relabel output sequence with sample_idPeter Amstutz
2020-06-18removed double sortingAndrea Guarracino
The -s argument in odgi build do the same thing that odgi sort -p s does.
2020-06-11tweaks for proper graph browser outputMichael R. Crusoe
2020-06-02update tool sub repoMichael R. Crusoe
2020-05-26Can have list of sequence labels to exclude from combined fastaPeter Amstutz
refs #68 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-14Workflow fixesPeter Amstutz
2020-05-11Merge pull request #49 from mr-c/add_pangenome_browser_prepPeter Amstutz
add pangenome browser prep
2020-05-05preserve the directory layout of segmentation.pyMichael R. Crusoe
2020-05-05move some tools into the shared repoMichael R. Crusoe
2020-05-04bump jerven/spodgi image to 0.0.6Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-04add pangenome browser prepMichael R. Crusoe
2020-05-04Increase RAM for minimap2Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-03Set a RAM requirement on odgi_to_rdf to influence it to run on c5Peter Amstutz
(because on a t3 it takes forever) Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-01Set verison tag on spodgi container imagePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-28Update spodgi docker imagePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Increase ram requirement for minimap2Peter Amstutz
Add --kickoff to immediately start an analysis workflow. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Workaround CWL limit by chunking file listPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Work around CWL content size limit by chunkingPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Add readsMergeDedup.fasta to outputPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Make sure there is a newline in relabeled fasta (but no blank lines)Peter Amstutz
2020-04-20Better handling of duplicate sequencesPeter Amstutz
Also save original fasta label in metadata
2020-04-20Relabel sequences to match metadata subjects.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Move workflows into main repoPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-05 18:41:57 +0000