| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |
| 2020-07-27 | new workflow for odgi building from spoa gfa | AndreaGuarracino | |
| 2020-06-18 | removed double sorting | Andrea Guarracino | |
| The -s argument in odgi build do the same thing that odgi sort -p s does. | |||
| 2020-05-26 | Can have list of sequence labels to exclude from combined fasta | Peter Amstutz | |
| refs #68 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-05-14 | Workflow fixes | Peter Amstutz | |
| 2020-05-11 | Merge pull request #49 from mr-c/add_pangenome_browser_prep | Peter Amstutz | |
| add pangenome browser prep | |||
| 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 | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-05-04 | add pangenome browser prep | Michael R. Crusoe | |
| 2020-05-04 | Increase RAM for minimap2 | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-05-03 | Set a RAM requirement on odgi_to_rdf to influence it to run on c5 | Peter Amstutz | |
| (because on a t3 it takes forever) Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-05-01 | Set verison tag on spodgi container image | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-28 | Update spodgi docker image | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-21 | Increase ram requirement for minimap2 | Peter Amstutz | |
| Add --kickoff to immediately start an analysis workflow. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-21 | Workaround CWL limit by chunking file list | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-21 | Work around CWL content size limit by chunking | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-20 | Add readsMergeDedup.fasta to output | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 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 | |
| Also save original fasta label in metadata | |||
| 2020-04-20 | Relabel sequences to match metadata subjects. | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-20 | Move workflows into main repo | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
 |
index : bh20-seq-resource | |
| Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis |
| aboutsummaryrefslogtreecommitdiff |