Somatic workflow - tumour vs normal.
Unsure of the function of this workflow, but it does a bunch of analysis of a tumour sample vs a normal sample. Perhaps someone with more knowledge of these tools can update this readme file somewhere along the line.
Two libraries are used from the /shared/lib area, VarScan.v2.4.4.jar and picard.jar, along with a shared reference file in /shared/reference/, GCA_000001405.15_GRCh38_no_alt_analysis_set
The two input files expected are named tumour.bam and normal.bam, in the resources directory, so the definition of the inputs in the Rakeiora sandbox should define these accordingly, presumably with the tumour sample related to/dependent on the previously selected normal one.
Note that a bunch of vcfs come back into the results directory, and the contents of that directory will be copied to the jupyter hub area when the researcher runs a workflow in Rakeiora. So before this is run on real data, the kaitiaki of the data and the workflow reviewers need to be OK with that.
NeSI does not claim ownership or authorship of this workflow. Authorship credits will follow later.