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2020-11-11Support uploading new metadata onlyPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-10Valid uploads with sequence_label in PubSeq replaces old one.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-09Make it so "pangenome analysis" only runs collect-seqs.Peter Amstutz
Will ensure that metadata is kept up to date. GFA isn't being generated. Will introduce new workflow that uses from_sparql to analyze a subset. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
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
2020-08-20Update links to reflect latest workflowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-08-19Consolidate steps to scale graph generation workflowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-17Make sure move_fastq_to_fasta_results gets everythingPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-16Add "validated" and "running workflows" tables to statusanalysis-refactorPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-16Catch exceptionsPeter Amstutz
Add script to cleanup bad uploads. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-16Refactor analysis code into a classPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-08Add --revalidate and fix checking/updating properties.Peter Amstutz
2020-07-08Get count from arvadosPeter Amstutz
Separate pending/rejected tables "Lastest results" is latest successful run. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-07--print-status=html creates html reportPeter Amstutz
2020-07-05Add bh20-seq-analyzer --print-statusPeter Amstutz
Get status from new property "status: validated/rejected" Also store QC fail error message.
2020-07-03A little more loggingPeter Amstutz
2020-07-03Add --no-start-analysisPeter Amstutz
2020-06-22Adjust QC filter and relabel output sequence with sample_idPeter Amstutz
2020-06-22Better invalid sequence QC handlingPeter Amstutz
2020-06-22Handle upload & assembly of gzipped, paired-end fastqPeter Amstutz
2020-05-26Can have list of sequence labels to exclude from combined fastaPeter Amstutz
refs #68 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-14Switch fasta identifiers to use a real working URLPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-04Sort input to hopefully get container reusePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-04Remove debug flag from workflow submitPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Increase ram requirement for minimap2Peter Amstutz
Add --kickoff to immediately start an analysis workflow. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-13Add __init__.py and fix importsPeter Amstutz
2020-04-10Propagating metadata to output works now.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-10Improve fasta/fastq QCPeter Amstutz
2020-04-10Fix swapped fasta/fastqPeter Amstutz
Replace example sequence with COV19 reference instead of HIV. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-10Fix up fasta/fastq validationPeter Amstutz
2020-04-10Validate & propagate metadataPeter Amstutz
2020-04-09Propagate metadata to pangenome so it can be merged by workflowPeter Amstutz
2020-04-08Fastq now runs through fastq2fasta pipelinePeter Amstutz
then gets added to pangenome analysis.
2020-04-07Add metadata validation with schema-saladPeter Amstutz
2020-04-07limit 1Peter Amstutz
2020-04-07Copy recent results to a set destinationPeter 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.
2020-04-06Add service to automatically run a workflow on collections uploaded to a ↵Peter Amstutz
project.
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