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path: root/bh20sequploader/main.py
AgeCommit message (Collapse)Author
2020-11-11Support uploading new metadata onlyPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-06Uploader script improvementsPjotr Prins
2020-10-27Commented in uploader main.pyPjotr Prins
2020-09-04fixed bugs in in index management and type conversionAndreaGuarracino
2020-08-28local QC is optionalAndreaGuarracino
2020-08-28added control (locally and in the validation) that sample_id has to be the ↵AndreaGuarracino
same in the metadata and in the FASTA header #103
2020-08-28qc_fasta returns also the seq_type; verified that only one FASTA is sent at ↵AndreaGuarracino
a time; code cleaning
2020-08-26updated parameter nameAndreaGuarracino
2020-07-16Improve uploader reporting.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-08Give uploader an option to trust local validation (for batch imports)upload-download-statusPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-08Uploader checks for duplicatesPeter Amstutz
2020-07-07Use minimap2 instead of clustalw for fasta QCPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-05Add bh20-seq-analyzer --print-statusPeter Amstutz
Get status from new property "status: validated/rejected" Also store QC fail error message.
2020-07-03Add --skip-qc for faster batch importPeter Amstutz
2020-07-03Adding --skip-qcPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-03Fix single arg uploadPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-06-22Handle upload & assembly of gzipped, paired-end fastqPeter Amstutz
2020-05-29Improved error output for the web uploaderPjotr Prins
2020-05-28Web: debugging metadata submissionPjotr Prins
2020-05-28Uploader: validate metadata first (it is faster)Pjotr Prins
2020-04-30Handle running in a container with no usernamePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Work around CWL content size limit by chunkingPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Working on NCBI importPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Add ShEx validationPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-13Inject path to find module bh20sequploaderPjotr Prins
2020-04-13Add __init__.py and fix importsPeter Amstutz
2020-04-13Closes #5Pjotr Prins
2020-04-10Fix up fasta/fastq validationPeter Amstutz
2020-04-10Validate & propagate metadataPeter Amstutz
2020-04-10Merge pull request #6 from uniqueg/fa_fq_validationPjotr Prins
validate seq format with magic file
2020-04-10Fixed TypeError: 'module' object is not callablePjotr Prins
2020-04-10validate seq format with magic fileAlex Kanitz
2020-04-09Moved Guix documentation into separate file (as it confused people ;)Pjotr Prins
2020-04-08Fastq now runs through fastq2fasta pipelinePeter Amstutz
then gets added to pangenome analysis.
2020-04-07Add metadata validation with schema-saladPeter Amstutz
2020-04-07Now moves collections into 'validated sequences' projectPeter 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 defaultPjotr Prins
- Disabled ssl checking which does not work if you lack a certificate
2020-04-06Add service to automatically run a workflow on collections uploaded to a ↵Peter Amstutz
project.
2020-04-06Now uploads dataPeter Amstutz
2020-04-06Start projectPeter Amstutz
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