Commit 1f7c07f7 authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Add scripts as inputs for rules

parent 18f88797
......@@ -3,7 +3,8 @@ from DP_classification.config import EXPERIMENT_DATA_DIR, DATA_PATH, DATASET_SOU
rule preprocess_clinical_patients:
input:
input:
'DP_classification/preprocessing/preprocess_clinical_file.py',
DATA_PATH / DATASET_SOURCE / 'clinical.csv',
DATA_PATH / DATASET_SOURCE / 'slides_filename_uuid.csv'
output:
......@@ -14,6 +15,7 @@ rule preprocess_clinical_patients:
rule compute_patients:
input:
'DP_classification/preprocessing/compute_patients.py',
EXPERIMENT_DATA_DIR / 'metadata_patients.csv',
expand(str(EXPERIMENT_DATA_DIR / '{split_id}' / 'gene_tr.txt'), split_id=[i for i in range(10)]),
expand(str(EXPERIMENT_DATA_DIR / '{split_id}' / 'gene_ts.txt'), split_id=[i for i in range(10)])
......@@ -25,6 +27,7 @@ rule compute_patients:
rule svs_to_random_tiles:
input:
'DP_classification/preprocessing/svs_to_random_tiles.py',
EXPERIMENT_DATA_DIR / 'metadata_patients.csv',
ancient(SVS_DIR), # ancient --> do not consider timestamp
output:
......
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