Updated analysis: Update oncoprint landscape module to use hotspot consensus maf

[cbethell]

What analysis module should be updated and why?

The oncoprint-landscape module should be updated to use the hotspot consensus maf file (as noted in #968 (comment)) once available.

What changes need to be made? Please provide enough detail for another participant to make the update.

The run-oncoprint.sh script will need to be updated to replace the current pbta-snv-consensus-mutation.maf.tsv.gz maf file with the hotspot consensus maf file for implementation, once available.

What input data should be used? Which data were used in the version being updated?

pbta-snv-hotspots-plus-consensus.maf.tsv.gz (replacing the current pbta-snv-consensus-mutation.maf.tsv.gz file being implemented)

When do you expect the revised analysis will be completed?

~ 1 day once the hotspot consensus maf file becomes available

Who will complete the updated analysis?

Likely @cbethell or someone at the CCDL

[jharenza]

Also adding that we should also switch to using the seg file and setting a threshold for amplifications (so gains and amps are not all coded as amp) once #987 is merged

[jharenza]

Note: since the consensus and hotspot maf are separate, this would require combining them and removing redundant calls.

[jharenza]

closed with #1088