Complete basic cancer use case end-to-end test

[holtgrewe]

Is your feature request related to a problem? Please describe. We need to create a minimal cancer variant calling pipeline use case setup here

• https://github.com/bihealth/snappy-use-case-cancer

Describe the solution you'd like We should have the following steps

• ngs_mapping
• somatic_variant_calling

for two or three public cancer exome data sets This could come from public data (ideally) or access-restricted. We could use two germline exomes and use one as proxy cancer and one as proxy tumor. We need to get this done end-to-end and then can refine (refinement out of scope). Data and static data should be downloaded either directly public data or can be deposited on our public file servers.

Describe alternatives you've considered N/A

Additional context N/A

[mbenary]

I would include RNA sequencing in the cancer use case as well. In addition, the following steps should be included

• hla_typing
• gene_expression_quantification
• somatic_targeted_seq_cnv_calling
• variant_annotation
• variant_filtration
• cbioportal_export (=variant-export)

[holtgrewe]

I adjusted my text for copy-and-paste issues.

Let's define "micro milestones" and convert each into a ticket.

e.g.,

• [ ] micro milestone: minimal
  • [ ] ngs_mapping
  • [ ] somatic_variant_calling
• [ ] micro milestone: basic cBioPortal export
  • [ ] somatic_variant_annotation
  • [ ] somatic_variant_filtration
  • [ ] cbioportal_export
• [ ] micro mileston: CNV calling
  • [ ] ...

etc.