This script can be used to (interactively) download the required umccrise/DragenWTS/arriba inputs from GDS for local testing/debugging, and to further render the RMarkdown report. Basic steps are:
Specify SBJ IDs of interest
Filter the Athena data_portal_workflow table for RNAsum workflows run on those SBJs (using {RAthena})
Grab the required metadata from the above table, such as gds_indir_dragen, gds_indir_umccrise, gds_indir_arriba, which point to GDS locations of the aforementioned inputs.
Now in each of those GDS directories, search for files matching a certain pattern, and download locally to a file structure matching GDS but from a localy root you specify (/path/to/rnasum/nogit/patient_data for me below).
Then since you have all the paths to the downloaded files, you can submit those to the RNAsum::rnasum_rmd function to render the RMarkdown report.
This script can be used to (interactively) download the required umccrise/DragenWTS/arriba inputs from GDS for local testing/debugging, and to further render the RMarkdown report. Basic steps are:
data_portal_workflowtable for RNAsum workflows run on those SBJs (using {RAthena})gds_indir_dragen,gds_indir_umccrise,gds_indir_arriba, which point to GDS locations of the aforementioned inputs./path/to/rnasum/nogit/patient_datafor me below).RNAsum::rnasum_rmdfunction to render the RMarkdown report.