Age | Commit message (Collapse) | Author | |
---|---|---|---|
2020-11-13 | there can be two specimen terms | AndreaGuarracino | |
2020-11-13 | Yaml and ShEx changes | lltommy | |
2020-11-12 | added closed shapes | AndreaGuarracino | |
2020-11-12 | added missing _type: "@id" to the assembly_method field in the schema | AndreaGuarracino | |
2020-11-12 | Trying to fix the submitter shape, shex and yaml | lltommy | |
2020-11-12 | Proposed new technology shape/yaml structure | lltommy | |
2020-11-11 | Support uploading new metadata only | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-11-11 | Documenting and QC of YAML. Some conflicts discovered that need review | lltommy | |
2020-11-11 | Merge branch 'master' of https://github.com/arvados/bh20-seq-resource | lltommy | |
2020-11-11 | restricting specimen_source to obo:NCIT which would have prevented the ncbi ↵ | lltommy | |
taxon bug | |||
2020-11-07 | RDF: use URIs | Pjotr Prins | |
2020-11-07 | Fixed the License error (https!!) | Pjotr Prins | |
2020-11-06 | Uploader script improvements | Pjotr Prins | |
2020-11-04 | fixed sequence_assembly_method field description | AndreaGuarracino | |
2020-10-27 | Commented in uploader main.py | Pjotr Prins | |
2020-10-01 | sequence divergence to 5% for minimap2 in the FASTA quality control | AndreaGuarracino | |
2020-10-01 | show more information in the error messages | AndreaGuarracino | |
2020-09-04 | fixed bugs in in index management and type conversion | AndreaGuarracino | |
2020-08-28 | local QC is optional | AndreaGuarracino | |
2020-08-28 | added control (locally and in the validation) that sample_id has to be the ↵ | AndreaGuarracino | |
same in the metadata and in the FASTA header #103 | |||
2020-08-28 | qc_fasta returns also the seq_type; verified that only one FASTA is sent at ↵ | AndreaGuarracino | |
a time; code cleaning | |||
2020-08-28 | fixed local QC, modifying the regex for FASTA/FASTQ to be more general | AndreaGuarracino | |
2020-08-26 | updated parameter name | AndreaGuarracino | |
2020-08-26 | typos in the code; little code refactoring | AndreaGuarracino | |
2020-08-24 | reverted the relaxation on the location attribute | AndreaGuarracino | |
2020-08-22 | Relaxing the location attribute | Pjotr Prins | |
2020-07-16 | Report similarity == 0 | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-07-16 | Improve uploader reporting. | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-07-16 | Make license optional | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-07-16 | Make license optional for now | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-07-16 | Make license optional for now | Pjotr Prins | |
2020-07-15 | License RDF | Pjotr Prins | |
2020-07-15 | Add RDF output | Pjotr Prins | |
2020-07-15 | Web: add license to input form | Pjotr Prins | |
2020-07-13 | Add ontology and schema for license information. For review. | Pjotr Prins | |
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 | 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 | Hack in a valid-uri check | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-07-07 | minimap2 returns nothing when there is no alignment. | 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 qc_fasta bug closing stream. | Peter Amstutz | |
2020-07-03 | Fix single arg upload | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-06-22 | Better invalid sequence QC handling | Peter Amstutz | |
2020-06-22 | Handle upload & assembly of gzipped, paired-end fastq | Peter Amstutz | |
2020-05-29 | Changed doc comment in schema | Pjotr Prins | |