Package: miniwdl-omics-run
miniwdl-omics-runThis command-line tool makes it easier to launchWDLruns on theAWS HealthOmicsworkflow service. It usesminiwdllocally to register WDL workflows, validate command-line inputs, and start a run.pip3 install miniwdl-omics-run

miniwdl-omics-run \
    --role-arn {SERVICE_ROLE_ARN} \
    --output-uri s3://{BUCKET_NAME}/{PREFIX} \
    {MAIN_WDL_FILE} input1=value1 input2=value2 ...Quick startPrerequisites: Unix command line with Python & pip; up-to-dateAWS CLIinstalled locally, andconfiguredwith full access to your AWS account.First a few one-time account setup steps (S3 bucket, IAM service role, ECR repo), then launching a test workflow.S3 bucketCreate an S3 bucket with a test input file.AWS_ACCOUNT_ID=$(aws sts get-caller-identity --query Account --output text)
AWS_DEFAULT_REGION=$(aws configure get region)

aws s3 mb --region "$AWS_DEFAULT_REGION" "s3://${AWS_ACCOUNT_ID}-${AWS_DEFAULT_REGION}-omics"
echo test | aws s3 cp - s3://${AWS_ACCOUNT_ID}-${AWS_DEFAULT_REGION}-omics/test/test.txtService roleCreate an IAM service role for your Omics workflow runs to use (to access S3, ECR, etc.).aws iam create-role --role-name poweromics --assume-role-policy-document '{
    "Version":"2012-10-17",
    "Statement":[{
        "Effect":"Allow",
        "Action":"sts:AssumeRole",
        "Principal":{"Service":"omics.amazonaws.com"}
    }]
}'

aws iam attach-role-policy --role-name poweromics \
    --policy-arn arn:aws:iam::aws:policy/PowerUserAccessWARNING:PowerUserAccess, suggested here only for brevity, is far more powerful than needed. SeeOmics docs on service rolesfor the least privileges necessary, especially if you plan to use third-party WDL and/or Docker images.ECR repositoryCreate an ECR repository suitable for Omics to pull Docker images from.aws ecr create-repository --repository-name omics
aws ecr set-repository-policy --repository-name omics --policy-text '{
    "Version": "2012-10-17",
    "Statement": [{
        "Sid": "omics workflow",
        "Effect": "Allow",
        "Principal": {"Service": "omics.amazonaws.com"},
        "Action": [
            "ecr:GetDownloadUrlForLayer",
            "ecr:BatchGetImage",
            "ecr:BatchCheckLayerAvailability"
        ]
    }]
}'Push a plain Ubuntu image to the repository.ECR_ENDPT="${AWS_ACCOUNT_ID}.dkr.ecr.${AWS_DEFAULT_REGION}.amazonaws.com"
aws ecr get-login-password | docker login --username AWS --password-stdin "$ECR_ENDPT"

docker pull ubuntu:22.04
docker tag ubuntu:22.04 "${ECR_ENDPT}/omics:ubuntu-22.04"
docker push "${ECR_ENDPT}/omics:ubuntu-22.04"Run test workflowpip3 install miniwdl-omics-run
wget https://raw.githubusercontent.com/miniwdl-ext/miniwdl-omics-run/main/test/TestFlow.wdl

miniwdl-omics-run TestFlow.wdl \
    input_txt_file="s3://${AWS_ACCOUNT_ID}-${AWS_DEFAULT_REGION}-omics/test/test.txt" \
    docker="${AWS_ACCOUNT_ID}.dkr.ecr.${AWS_DEFAULT_REGION}.amazonaws.com/omics:ubuntu-22.04" \
    --role poweromics --output-uri "s3://${AWS_ACCOUNT_ID}-${AWS_DEFAULT_REGION}-omics/test/out"This zips upthe specified WDL, registers it as an Omics workflow, validates the given inputs, and starts the workflow run.The WDL source code may be set to a local filename or a public HTTP(S) URL. The tool automatically bundles any WDL files imported by the main one. On subsequent invocations, it'll reuse the previously-registered workflow if the source code hasn't changed.The command-line interface accepts WDL inputs using theinput_key=valuesyntax exactly likeminiwdl run, including the option of a JSON file with--input FILE.json. Each input File must be set to an existing S3 URI accessible by the service role.AdviceOmics can use Docker imagesonlyfrom your ECR in the same account & region.This often means pulling, re-tagging, and pushing images as illustrated above withubuntu:22.04.And editing any WDL tasks that hard-code docker image tags to take them as inputs instead.Each ECR repository must have the Omics-specific repository policy set as shown above.We therefore tend to use a single ECR repository for multiple Docker images, disambiguating them using lengthier tags.If you prefer to use per-image repositories, just remember to set the repository policy on each one.To quickly list a workflow's inputs, tryminiwdl run workflow.wdl ?