| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2020-08-28 | qc_fasta returns also the seq_type; verified that only one FASTA is sent at ↵ | AndreaGuarracino | |
| a time; code cleaning | |||
| 2020-08-26 | updated parameter name | AndreaGuarracino | |
| 2020-07-16 | Improve uploader reporting. | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 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 | |
| 2020-07-07 | Use minimap2 instead of clustalw for fasta QC | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-07-05 | 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 | 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 single arg upload | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-06-22 | Handle upload & assembly of gzipped, paired-end fastq | Peter Amstutz | |
| 2020-05-29 | Improved error output for the web uploader | Pjotr Prins | |
| 2020-05-28 | Web: debugging metadata submission | Pjotr Prins | |
| 2020-05-28 | Uploader: validate metadata first (it is faster) | Pjotr Prins | |
| 2020-04-30 | Handle running in a container with no username | 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> | |||
| 2020-04-21 | Working on NCBI import | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-20 | Add ShEx validation | Peter Amstutz | |
| Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
| 2020-04-13 | Inject path to find module bh20sequploader | Pjotr Prins | |
| 2020-04-13 | Add __init__.py and fix imports | Peter Amstutz | |
| 2020-04-13 | Closes #5 | Pjotr Prins | |
| 2020-04-10 | Fix up fasta/fastq validation | Peter Amstutz | |
| 2020-04-10 | Validate & propagate metadata | Peter Amstutz | |
| 2020-04-10 | Merge pull request #6 from uniqueg/fa_fq_validation | Pjotr Prins | |
| validate seq format with magic file | |||
| 2020-04-10 | Fixed TypeError: 'module' object is not callable | Pjotr Prins | |
| 2020-04-10 | validate seq format with magic file | Alex Kanitz | |
| 2020-04-09 | Moved Guix documentation into separate file (as it confused people ;) | Pjotr Prins | |
| 2020-04-08 | Fastq now runs through fastq2fasta pipeline | Peter Amstutz | |
| then gets added to pangenome analysis. | |||
| 2020-04-07 | Add metadata validation with schema-salad | Peter Amstutz | |
| 2020-04-07 | Now moves collections into 'validated sequences' project | Peter Amstutz | |
| Improve logging for seq service Fix uploader bug Runs workflow with all validated sequences. | |||
| 2020-04-06 | - Added some output and run main() by default | Pjotr Prins | |
| - Disabled ssl checking which does not work if you lack a certificate | |||
| 2020-04-06 | Add service to automatically run a workflow on collections uploaded to a ↵ | Peter Amstutz | |
| project. | |||
| 2020-04-06 | Now uploads data | Peter Amstutz | |
| 2020-04-06 | Start project | Peter Amstutz | |
 |
index : bh20-seq-resource | |
| Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis |
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