Single/multi-sample option-dependent inputs for subclonal deconvolution.

[nicola-calonaci]

The SUBCLONAL_DECONVOLUTION sub-workflow should take as input both a single-sample and a multi-sample (if applicable) output from the CNAqc sub-workflow, and run with the following possible --tools:

• Single sample:
  • Mobsterh
  • Pyclone
  • VIBER
• Multi-sample:
  • Mobsterh+Pyclone
  • Mobsterh+VIBER
  • Pyclone
  • VIBER

In the case of Mobsterh+, the user should be able to either:

• use all the mutations
• use all mutations except the ones assigned to Tail in EVERY sample

In all cases, the user should be able to choose a filtering strategy based on the CNAqc tests.

[nicola-calonaci]

UPDATE:

The SUBCLONAL_DECONVOLUTION sub-workflow should take as input only a multi-sample CNAqc object. This will contain, for each sample, a field with mutations mapped to private segments (see #28).

Starting from this, you should develop a small module that rebuilds the original single-sample CNAqc object, and is used if the single-sample condition is met.