Add tumour-only mode

[RaqManzano]

Description of feature

Generate tumour-only mode for variant calling. This should only affect to the variant_calling module of the pipeline, once we obtain the VCFs the rest of modules should behave the same.

TODOs:

• Review tumour-only subworkflows from sarek, starting from bam_variant_calling_tumor_only_all
• Add the appropriate subworkflows for the pipeline
• Create SAGE tumour only subworkflow
• Testing
• Check filtering in case some adjustments need to be done

[RaqManzano]

Have a working version of tumour only in a local branch, will push when testing is done.

[hajdylaf]

Hi! Any developments on this feature? I'd like to run some of my tumor-only samples through the pipeline 😄

[RaqManzano]

A draft pull request is now live #43

[chstubbe]

Hi! I am also interested in this workflow for tumour only samples, any updates? Can I find it to test? Thank you!