Rule check for pipeline inputs from S3 missing

[jaamarks]

We’ve built rules that check Nextflow code for patterns that violate HealthOmics environment policies.

For example, one rule checks that pipeline inputs are loaded from Amazon Simple Storage Service (Amazon S3) buckets, or >HealthOmics Sequence Stores, and that pipeline container images are being pulled from Amazon ECR Private repositories.

• https://aws.amazon.com/blogs/hpc/linter-rules-for-nextflow-to-improve-the-detection-of-errors-before-runtime/

But I don't see a rule for this in linter-rules/src/main/groovy/software/amazon/nextflow/rules/healthomics. Is this in the works?

[markjschreiber]

The rule to check for ECR URIs is this one: https://github.com/awslabs/linter-rules-for-nextflow/blob/main/linter-rules/src/main/groovy/software/amazon/nextflow/rules/healthomics/ContainerUriRule.groovy

[markjschreiber]

I think you are right though. I don't see one for S3 paths. Not sure if this was in a branch that we never pushed or was something that was never created. I will create an issue.