Somatic pipeline development branch

[ericblanc20]

The somatic pipeline should undergo major changes/developments. Many of these changes are inter-connected and break the current code (for example wrappers shared between steps, changes in panel of normals, ...).

For this reason, it would be helpful to create a development branch, specially for the large changes in development. This would protect the main branch from breaking changes and facilitate the pull request reviews: large changes affecting multiple steps could be split into logical chunks, even if they leave the whole of snappy in a broken state.

The current short term plan would be:

• Create a somatic_cnv_calling step for both WES & WGS
• Implement there support for cnvkit tool (including B-allele fractions)
• Adapt the panel_of_normals step for the updated cnvkit wrappers (& potentially other necessary changes)
• Include the other WES & WGS tools
• Include ascat (an older implementation already exists in step somatic_purity_ploidy_estimate)
• Revive somatic_wgs_sv_calling (I am not sure that a somatic_targeted_seq_sv_calling step is achievable)

Many of these actions are already in progress.

In the longer term (possibly outside of the scope of this issue):

• Refactor the ngs_mapping step
• Include a pathway_activity step for bulk mRNA expression
• Refactor (somatic?) variant filtration using vembrane, and improve filtration guidelines
• Revisit viral/bacterial/contaminant sequences detection