Update /dap/submit endpoint to utilize the new AWS Batch pipeline submission#277
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…return job information rather than submitting to EC2
thecaffiend
approved these changes
Aug 20, 2025
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This updates the
/dap/submitAPI endpoint to submit Nextflow jobs to the AWS Batch workflow job queue and return the created job information.Testing
Make a POST request to
https://api.cape-dev.org/capi-dev/dap/submitwith the request body of:{ "pipelineName": "bactopia/bactopia", "pipelineVersion": "v3.0.1", "outputPath": "s3://ccd-dlh-t-genomics-result-raw-vbkt-s3-5d4efd2/pipeline-output", "nextflowOptions": "--max_cpus 8 --max_memory 24 --r1 s3://ccd-dlh-t-genomics-input-raw-vbkt-s3-b4b66f9/fastx/ERR10167837_1.fastq.gz --r2 s3://ccd-dlh-t-genomics-input-raw-vbkt-s3-b4b66f9/fastx/ERR10167837_2.fastq.gz --sample ERR10167837" }Verify you get a successful response back and check the workflow queue in AWS Batch to see if a job has started. (Optionally immediately kill the job so that we don't rack up charges, or watch the money burn)