VGP Assembly Pipeline Skill

Overview

The Vertebrate Genome Project (VGP) assembly pipeline consists of Galaxy workflows for producing high-quality, phased, chromosome-level genome assemblies. This skill covers workflow selection, execution patterns, and quality control checkpoints.

Supporting files (detailed reference material):

• RESOURCE_ANALYSIS.md - Workflow canonical names, official/non-official filtering, metric availability, tool-level resource optimization
• DATA_INTEGRATION.md - ToLID patterns, GenomeArk S3 integration, NCBI accession recovery, Meryl k-mer management, species-metrics merging
• QUALITY_VALIDATION.md - Curation impact analysis, GenomeScope data validation, assembly size interpretation, communication patterns

Pre-flight Checks Before Testing

VGP user accounts have a 250 GB quota. If quota_percent is at 100%, all new upload jobs land in paused state immediately and planemo dies with a cryptic message:

Exception: Upload job [...] failed with state [paused]

The error gives no hint that quota is the cause. Check before launching any planemo test: