This is a portion of a Snakefile that we used to automate QAM computations for a larger clinical study.
snakemake --profile profiles/local --directory ../../tests/test_data _output/Aggregated.xlsx
The folder structure has to be as follows (same as in the test data used in the repository):
+-- PatientID
| +-- LesionNr
| +-- [PatientID]_L[LesionNR]_Ablation.nii.gz
| +-- [PatientID]_L[LesionNR]_Liver.nii.gz
| +-- [PatientID]_L[LesionNR]_Tumor.nii.gz
For more information about Snakemake refer to their website https://snakemake.readthedocs.io.