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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>
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