fix: resolve S3 publishing failures and publishDir configuration casting errors

[edmundmiller]

Problem

Addresses two critical issues identified in the AWSMegatests workflow failures:

1. S3 Publishing Failures: workflow failing with S3 copy errors for large files
2. Configuration Casting Errors:

Root Causes

S3 Publishing Failures

• Missing S3 permissions for multipart upload operations (required for files >5GB)
• Current policy lacked: , , ,

Configuration Casting Errors

• Closures in publishDir configuration being cast as strings
• Problematic closures: , ,

Solution

Enhanced S3 Permissions

• Added multipart upload permissions to TowerForge S3 IAM policy
• Enables robust handling of large file publishing operations
• Updated policy version hash to trigger compute environment recreation

Fixed publishDir Configuration

• Removed problematic closures from publishDir tags in all environment configs
• Kept only static string values that don't require runtime evaluation
• Applied across CPU, GPU, and ARM compute environment configurations

Files Changed

• • Enhanced S3 IAM policy with multipart upload permissions
• • Fixed publishDir tags configuration across all environments

Testing

• Pulumi preview confirmed S3 policy updates and compute environment recreation
• All three compute environments will be replaced with updated configurations
• Policy version hash updated from to

Impact

• Resolves S3 publishing failures for large files (>5GB)
• Eliminates configuration casting errors in Nextflow workflows
• Ensures robust S3 operations with proper multipart upload support

Fixes the workflow failure reported by Seqera AI.

[edmundmiller]

Branch rebased onto latest main to resolve conflicts.