docs: add comprehensive secrets usage documentation

Add docs/secrets.md with detailed guidance on:
- Configuring workspace secrets with database credentials
- Setting up secrets in Seqera Platform
- Local development with Nextflow secrets command
- Troubleshooting common secrets configuration issues
- Error pattern identification and resolution

Update README.md to reference the new secrets documentation.

Provides users with complete guidance for secure credential management
in production deployments, especially for cloud databases like AWS Athena.

Signed-off-by: Edmund Miller <[email protected]>

Author: edmundmiller

README.md

@@ -57,6 +57,8 @@ The following options are available:
 `sql.db.'<DB-NAME>'.password`
 : The database connection password.
 
+For information on using secrets with database credentials, see [docs/secrets.md](docs/secrets.md).
+
 ## Dataflow Operators
 
 This plugin provides the following dataflow operators for querying from and inserting into database tables.

docs/secrets.md

@@ -0,0 +1,55 @@
+# Using Secrets for Database Credentials
+
+For production deployments, it's recommended to use Nextflow secrets instead of hardcoding credentials in configuration files. This is especially important when working with cloud databases like AWS Athena.
+
+## Configuration with Secrets
+
+When using [Nextflow secrets](https://www.nextflow.io/docs/latest/secrets.html) (available in Nextflow 25.04.0+), you can reference workspace or user-level secrets in your database configuration:
+
+```groovy
+sql {
+    db {
+        athena {
+            url = 'jdbc:awsathena://AwsRegion=us-east-1;S3OutputLocation=s3://bucket;Workgroup=CompBio'
+            user = secrets.ATHENA_USER
+            password = secrets.ATHENA_PASSWORD
+            driver = 'com.simba.athena.jdbc.Driver'
+        }
+    }
+}
+```
+
+## Setting Up Secrets in Seqera Platform
+
+1. **Workspace Secrets**: Navigate to your workspace → Secrets → Add secret
+2. **User Secrets**: Navigate to Your profile → Secrets → Add secret  
+3. Create secrets with names matching your configuration (e.g., `ATHENA_USER`, `ATHENA_PASSWORD`)
+
+## Troubleshooting Secrets Issues
+
+If you encounter authentication errors like "Missing credentials error", verify:
+
+- **Secret Names**: Ensure secret names in your configuration match exactly (case-sensitive)
+- **Permissions**: Verify you have access to workspace secrets or have defined user-level secrets
+- **Nextflow Version**: Secrets require Nextflow >=25.04.0
+- **Secret Values**: Ensure secrets contain valid credentials (no empty values)
+
+Common error patterns:
+- `user=sa; password=null` indicates secrets were not resolved
+- `Unresolved secret detected` means secret names don't match or aren't accessible
+
+## Local Development
+
+For local testing, you can use the Nextflow secrets command:
+
+```bash
+# Set secrets locally
+nextflow secrets set ATHENA_USER "your-username"  
+nextflow secrets set ATHENA_PASSWORD "your-password"
+
+# List secrets
+nextflow secrets list
+
+# Run pipeline with secrets
+nextflow run your-pipeline.nf
+```