Add cancer_type parameter

[bounlu]

It would be great to incorporate cancer_type information, if known, as a parameter into the pipeline for better biomarker identification / filtering / reporting rather than just using the generic “doid 162 cancer” here.

[scwatts]

Thanks for opening the issue @bounlu! This has previously been discussed to some extent and an implementation planned for passing the relevant parameter to the ORANGE process that utilises existing code to collect this information from the samplesheet on a per-tumor basis

/cc @rhassaine

[bounlu]

Good to know that it's already been considered in the pipeline. Can I directly use the DOIDs from here to test it in the pipeline? What are the full list of doids that are supported?

[rhassaine]

We have this list (for 37) @bounlu -doid.json

[bounlu]

Thanks for providing the file. I have extracted the important information and simplified as a 3-column TSV file: doid.txt