Age | Commit message (Collapse) | Author | |
---|---|---|---|
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 | |
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 | |
2020-05-06 | Adding additional frontend option (PATO_0001340) to QC | lltommy | |
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> | |||
2020-04-30 | Last addition/edits to the meta data schema | lltommy | |
2020-04-29 | Use subprocess invocation is backwards compatible with Python 3.5 | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-04-29 | Add reference | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-04-28 | Merge branch 'master' of https://github.com/arvados/bh20-seq-resource | lltommy | |
2020-04-28 | Decision to settle for float instead of integers for the coverage | lltommy | |
2020-04-28 | Call clustalw to compare sequence to reference | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-04-28 | Changes to the structure - we use lists now instead of strings where it ↵ | lltommy | |
makes sense. This allows us to have multiple values where in makes sense | |||
2020-04-23 | adding a submitter comment field | lltommy | |
2020-04-23 | Adding a third sequence technology option | lltommy | |
2020-04-23 | Merge branch 'master' into patch-3 | LLTommy | |
2020-04-22 | Fixing ShEx expression, one ? too much | lltommy | |
2020-04-22 | Forgot to add _id | lltommy | |
2020-04-22 | Including restrictions to the host status | lltommy | |
2020-04-22 | Small changes all around, trying to make the importer/metadata better | lltommy | |
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 | add noLinkCheck to specimen_source2 | Peter Amstutz | |
2020-04-21 | Tweak handling of "coverage" also fix typo | 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> | |||
2020-04-21 | Updated shex and manditory fields and stuff | lltommy | |
2020-04-20 | Reconsidered these should be noLinkCheck | Peter Amstutz | |
2020-04-20 | Add identity:true to collection_location | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-04-20 | Schema changes from @LLTommy | Peter Amstutz | |
2020-04-20 | Better handling of duplicate sequences | Peter Amstutz | |
Also save original fasta label in metadata | |||
2020-04-20 | Make doc not contradict option list | Adam Novak | |
2020-04-20 | Put back Intersex with the closest PATO equivalent | Adam Novak | |
These options still disagree with the doc string in the schema. | |||
2020-04-20 | Add ShEx validation | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-04-20 | Making collection date and collection location MANDATORY fields, turning ↵ | lltommy | |
orcid into IRI | |||
2020-04-20 | Fixing string -> URI in speciman, plus other things | lltommy | |
2020-04-19 | small updates to the yaml schema, updating the example files | lltommy | |
2020-04-19 | Updating NCBI dictonaries, adding UI options, small yaml schema changes | lltommy | |
2020-04-19 | Merge pull request #24 from adamnovak/dropdowns | Pjotr Prins | |
Add dropdown support to web uploader metadata form | |||
2020-04-18 | Extending yaml schema a bit and adding additional information for the UI | lltommy | |
2020-04-17 | Copy NCIT IRIs back to schema doc | Adam Novak | |
2020-04-17 | Spruce up the options file and add missing values | Adam Novak | |
2020-04-17 | Create option dropdowns from an options file | Adam Novak | |