Snakefile expects patients_rtstruct.txt file - no way to create this in codebase

[katy-scott]

patientFile = "metadata/patients_rtstruct.txt" with open(patientFile, 'r') as file: PATIENT_IDS = file.read().splitlines()

Lines 12-14 in Snakefile expect this metadata file that currently has RADCURE patient IDs in it, but no code exists in the repo to make this file for other datasets.

Either

• Add code to make this metadata file
• Change Snakefile to get PATIENT_IDS directly

[katy-scott]

could just be something as simple as
find rawdata/radiomics/HNSCC/ -maxdepth 1 -mindepth 1 -type d -printf '%f\n' > metadata/patients_rtstruct.txt

mindepth prevents the current directory from being included in the list