[User story] Small test data

[fellen31]

Need

As a developer, I need the pipeline to have a test profile with accompanying relevant test data, which should test if not all then at least the majority of the pipeline.

Suggested approach

Currently there are three presets available: pacbio, revio and ONT_R10. Using the revio preset should cover all pacbio cases.

Can be closed when

• [x] Tested with BAM input
  • [X] Revio
  • [x] ONT
• [x] Tested with fastq input
  • [X] Revio
  • [x] ONT
• [x] Tested with default parameters
  • [X] Revio
  • [x] ONT
• [x] Tested with one sample
  • [X] Revio
  • [x] ONT
• [x] Tested with multiple samples
  • [X] Revio
  • [x] ONT
• [x] Tested with multiple files per sample
  • [X] Revio
  • [x] ONT
• [x] Tested with --split_fastq > 1 
  • [X] Revio
  • [x] ONT
• [x] Tested with --parallel_snv 1
  • [X] Revio
  • [x] ONT
• [x] Tested with samples where sex=0
  • [X] Revio
  • [x] ONT
  • [x] Update somalier to v0.2.19 to prevent infer sex bug
• [x] Tested with BED
  • [X] Revio
  • [x] ONT
• [X] Tested without BED
  • [X] Revio
• [ ] #478

  Additional considerations

HIPHASE_SV takes input from both DeepVariant and an SV caller to phase reads. Sniffles is not supported and it will fail depending on how the calls in the VCF looks. Ideally the test data would maybe provide all possible types of SVs, because with the current test data HiPhase will not fail (or remove HiPhase, or add psbv as input which is the only supported SV-caller).

[fellen31]

Added working revio test data in #33. Points above still valid.

If possible, the test data should also be able to:

• Assemble both haplotypes

[fellen31]

Adding CNV-workflow as separate issue (#60)

[fellen31]

Add SNV-annotation to test profile as separate issue (#74)