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AgeCommit message (Expand)Author
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.•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-11-18Fix typo. Give from_sparql more RAM.•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-11-18Add query-to-gfa workflow•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-11-11Make collect-seqs skip bad inputs.•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-11-10Use arvados uuids for RDF subjects.•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> uuid-for-resourcePeter Amstutz
2020-11-09Make resource link work for both portable data hashes and sample id•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-11-09Rename schema param to metadataSchema•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-11-09Extract subset of the all-sequences fasta by running a sparql query.•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-09-26script for processing the metadata of the ESR samples; moved delete_entries_o...AndreaGuarracino
2020-08-28added script to remove entries on ArvadosAndreaGuarracino
2020-08-26Increase RAM for odgi-build-from-spoa-gfa•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-08-25Increase RAM requirement for sort_fasta_by_quality_and_len•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-08-19Fix output parameters•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-08-19Scaling pangenome generation•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-08-19Consolidate steps to scale graph generation workflow•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
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 over...AndreaGuarracino
2020-07-27added spoa workflow in a low memory consumption modeAndreaGuarracino
2020-07-27new workflow for odgi building from spoa gfaAndreaGuarracino
2020-06-18removed double sorting•••The -s argument in odgi build do the same thing that odgi sort -p s does.Andrea Guarracino
2020-05-26Can have list of sequence labels to exclude from combined fasta•••refs #68 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-05-14Workflow fixesPeter Amstutz
2020-05-11Merge pull request #49 from mr-c/add_pangenome_browser_prep•••add pangenome browser prepPeter Amstutz
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 0.0.6•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-05-04add pangenome browser prepMichael R. Crusoe
2020-05-04Increase RAM for minimap2•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-05-03Set a RAM requirement on odgi_to_rdf to influence it to run on c5•••(because on a t3 it takes forever) Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-05-01Set verison tag on spodgi container image•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-28Update spodgi docker image•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-21Increase ram requirement for minimap2•••Add --kickoff to immediately start an analysis workflow. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-21Workaround CWL limit by chunking file list•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-21Work around CWL content size limit by chunking•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-20Add readsMergeDedup.fasta to output•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-20Make sure there is a newline in relabeled fasta (but no blank lines)Peter Amstutz
2020-04-20Better handling of duplicate sequences•••Also save original fasta label in metadata Peter Amstutz
2020-04-20Relabel sequences to match metadata subjects.•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-20Move workflows into main repo•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
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