Primary Care public workflow aka pharmacogenomic
NeSI does not claim ownership or authorship of this workflow. Authorship credits will follow later.
Based on Ben Halliday's work.
Adjusted to be used within Rakeiora by Matt Pestle.
The defined input for this workflow in Rakeiora should be variants, multi-selected, merged globally into a file named whatever the value of inputvcffile in the config.yaml nominates.
The bedfile used when running the workflow should match that of the gene specified in the ALLELES variable. The values of this variable should be uniform in the gene portion and the appropriate/corresponding files must be present in the pharmvar data.
This bedfile can be determined at [Rakeiora test - gene bedefile] (https://test.data.nesi.org.nz/app/sandbox/gene.xsql) You will need to tick the "drop chr" option.
You can peruse this data from your jupyter hub in the Rakeiora test area - [Rakeiora test] (https://test.data.nesi.org.nz)
Rakeiora will retrieve the bedfile specified regions for the sample selected and merge them using bcftools into a file named as you specify.
DRUGS should be in the "drug(s)" column of pharmgkb file specified in the config.yaml (also perusable from the /shared area in the jupyter hub of Rakeiora test area)
The GetDrugList Rule currently just generates random data. It will be replaced with calls to ALEA to get real data once all the necessary security and setup steps are done.