| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2020-07-12 | Remove duplicate counter | Pjotr Prins | |
| 2020-07-12 | Remove duplicate counter | Pjotr Prins | |
| 2020-07-10 | metadata with missing host_species are not created | AndreaGuarracino | |
| 2020-07-10 | an output file is created with the accessions for which no YAML file is created | AndreaGuarracino | |
| 2020-07-10 | updated metadata source | AndreaGuarracino | |
| 2020-07-10 | other term for Homo sapiens (for SRA samples) | Andrea Guarracino | |
| 2020-07-09 | Skip certificate check - this was upstreamed in Arvados, so we can remove later | Pjotr Prins | |
| 2020-07-09 | Merge pull request #93 from AndreaGuarracino/patch-22 | Pjotr Prins | |
| fixed bug that lead to invalid sample_sequencing_technology values | |||
| 2020-07-09 | fixed bug that lead to invalid sample_sequencing_technology values | Andrea Guarracino | |
| 2020-07-08 | Adding missing GPS coordinates et all | lltommy | |
| 2020-07-08 | Try to fix lab_address wrong predicate, fix submitter shape on the way and ↵ | lltommy | |
| hopefully brought it in synch with the yaml | |||
| 2020-07-08 | Merge pull request #92 from arvados/upload-download-status | Peter Amstutz | |
| Split upload tab. Add upload status tab. Also a bunch of QC and uploader improvements. | |||
| 2020-07-08 | Give uploader an option to trust local validation (for batch imports)upload-download-status | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-07-08 | Uploader checks for duplicates | Peter Amstutz | |
| 2020-07-08 | Avoid redundant loading of schema | Peter Amstutz | |
| 2020-07-08 | Add --revalidate and fix checking/updating properties. | Peter Amstutz | |
| 2020-07-08 | Hack in a valid-uri check | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-07-08 | Get count from arvados | Peter Amstutz | |
| Separate pending/rejected tables "Lastest results" is latest successful run. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-07-08 | Fetch status as anonymous user | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-07-08 | Split upload tab. Add upload status tab. | Peter Amstutz | |
| Add more direct links on download page. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-07-08 | Merge pull request #89 from proccaserra/patch-1 | LLTommy | |
| Update form.html | |||
| 2020-07-07 | Merge branch 'master' of https://github.com/arvados/bh20-seq-resource | lltommy | |
| 2020-07-07 | Adding some more country labels. Some GPS are still missing, will handle in ↵ | lltommy | |
| the future | |||
| 2020-07-07 | Adding sequencer labels | lltommy | |
| 2020-07-07 | Merge pull request #90 from AndreaGuarracino/patch-21 | LLTommy | |
| genbank and sra scripts update, new terms in the ontology dictionaries | |||
| 2020-07-07 | --print-status=html creates html report | Peter Amstutz | |
| 2020-07-07 | fix missing authors #91 | AndreaGuarracino | |
| 2020-07-07 | minimap2 returns nothing when there is no alignment. | Peter Amstutz | |
| 2020-07-07 | if the technology is not found, the YAML file is not created; managed longer ↵ | AndreaGuarracino | |
| species strings | |||
| 2020-07-07 | Use minimap2 instead of clustalw for fasta QC | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-07-06 | renamed sra script; added seq technology in its additional information field ↵ | AndreaGuarracino | |
| if the term … | |||
| 2020-07-06 | fix ncbi_countries dictionary | AndreaGuarracino | |
| 2020-07-06 | new terms in the ncbi_countries dictionary | Andrea Guarracino | |
| 2020-07-06 | added seq technology in its additional information field if the term is ↵ | AndreaGuarracino | |
| missing in the dicts | |||
| 2020-07-06 | updated SraExperimentPackage info | AndreaGuarracino | |
| 2020-07-06 | two more terms in the ncbi_sequencing_technology dictionary | Andrea Guarracino | |
| 2020-07-06 | fixed bugs in the download_sra_data | Andrea Guarracino | |
| 2020-07-06 | new terms in the sequencing_technology dictionary | Andrea Guarracino | |
| 2020-07-05 | Add bh20-seq-analyzer --print-status | Peter Amstutz | |
| Get status from new property "status: validated/rejected" Also store QC fail error message. | |||
| 2020-07-03 | A little more logging | Peter Amstutz | |
| 2020-07-03 | Add upload.cwl | Peter Amstutz | |
| 2020-07-03 | Add --no-start-analysis | Peter Amstutz | |
| 2020-07-03 | Add --skip-qc for faster batch import | Peter Amstutz | |
| 2020-07-03 | Adding --skip-qc | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-07-03 | Fix qc_fasta bug closing stream. | Peter Amstutz | |
| 2020-07-03 | Improving genbank import workflow | Peter Amstutz | |
| 2020-07-03 | Fix single arg upload | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-07-03 | Update form.html | Philippe Rocca-Serra | |
| s/onthology/ontology/ | |||
| 2020-06-25 | Update labels.ttl | LLTommy | |
| adding label for "Illumina HiSeq X" | |||
| 2020-06-24 | Merge pull request #87 from AndreaGuarracino/patch-20 | LLTommy | |
| added script to crete metadata for SRA data; new dictionary entries; little directory changes | |||
 |
index : bh20-seq-resource | |
| Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis |
| aboutsummaryrefslogtreecommitdiff |