Annotation Workflow

Annotation Wdl

Description:

Describes structure of a genome assembly by marking locations of genes.

Inputs:

• BV-BRC Assembly Filepath (string)
  • This workspace path is an output of the assembly workflow
• Sample Name (string)
• Scientific Name (string)
• BV-BRC Username (string)
• BV-BRC Password (string)
• Timestamp (integer)
  • Timestamp from assembly workflow output, used for BV-BRC file management

Input JSON Template:

{

  "annotation_analysis.bvbrc_assembly_path": "ws:bvbrc/workspace/path/to/assembly.fastq",

  "annotation_analysis.sample_name": "SampleName",

  "annotation_analysis.scientific_name": "ScientificName",

  "annotation_analysis.BVBRC_user": "username",

  "annotation_analysis.BVBRC_password": "password",

  "annotation_analysis.timestamp": "SampleName"

}

Output:

• Assembly (file)
  • Assembly file compressed with Gzip
• Assembly Bandage Plot (file, SVG)

Task Wdls

• BV-BRC-Annotation-Task

• Plasmidfinder Task