Support cloud storage URIs (gs://, s3://) in CSV samplesheets

[ikhrustalev]

Feature request

Currently, CSV samplesheets only support local filesystem paths in path_prefix. Users working with cloud storage must use the JSON samplesheet format instead. It would be convenient to support cloud URIs (gs://, s3://, etc.) directly in CSV samplesheets.

Motivation

• CSV samplesheets are simpler to generate and more widely used
• Many production pipelines store genotype data in cloud buckets and generate samplesheets dynamically
• The JSON format works as a workaround but requires a different structure (geno/pheno/variants fields instead of path_prefix)

Current behavior

SamplesheetParser.resolvePath() treats any path not starting with / as relative and resolves it against the samplesheet's parent directory. A path_prefix like gs://bucket/path/sample becomes /local/dir/gs:/bucket/path/sample.

Suggested fix

Detect URI schemes in resolvePath() and return them as-is, skipping relative path resolution:

private def resolvePath(path) {
    if (path.matches('^[a-zA-Z][a-zA-Z0-9+.-]*://.*')) {
        return path
    }
    // existing logic...
}

Happy to contribute a PR for this if it's welcome.