Implement a wizard or procedure for registering FASTQ files for WGS

[Nicklas Nordborg]

We are sending samples to an external lab for WGS. When we receive the FASTQ files with the result we need a simple procedure or wizard that is NOT including several manual steps and batch imports from Excel files.

Right now we have aliquots from DNA (normal and tumor) and we need to create items and annotations:

• Library items
  • Pipeline
  • ExternalOperator
• MergedSequences items
  • Pipeline
  • DataFilesFolder
  • READS
• FASTQ file items
  • FlowCellID
  • FlowCellType
  • LaneNumber
  • READS
  • ReadLength
  • SequencingRunNumber
  • SerialNumber

Most information can be extracted from the FASTQ files. We are not sure if the FASTQ files have merged data from different sequencing runs. In that case we may want to split them per flow cell and lane so that they are compatible with existing data.