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Fix bug of params in Snakefile for days_to_analyse

pull/95/head
Meng Li 2020-04-16 14:42:44 -04:00
parent 5696b4f6d4
commit 77d41639d8
1 changed files with 4 additions and 4 deletions
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8
Snakefile
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@ -10,10 +10,10 @@ rule all:
input: input:
# My study (this is an example of a rule created specifically for a study) # My study (this is an example of a rule created specifically for a study)
expand("data/interim/{pid}/days_to_analyse_{days_before_surgery}_{days_in_hospital}_{days_after_discharge}.csv", expand("data/interim/{pid}/days_to_analyse_{days_before_surgery}_{days_in_hospital}_{days_after_discharge}.csv",
pid=config["PIDS"], pid = config["PIDS"],
days_before_surgery = config["PARAMS_FOR_ANALYSIS"]["DAYS_BEFORE_SURGERY"], days_before_surgery = config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_BEFORE_SURGERY"],
days_after_discharge= config["PARAMS_FOR_ANALYSIS"]["DAYS_AFTER_DISCHARGE"], days_after_discharge = config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_AFTER_DISCHARGE"],
days_in_hospital= config["PARAMS_FOR_ANALYSIS"]["DAYS_IN_HOSPITAL"]), days_in_hospital = config["PARAMS_FOR_ANALYSIS"]["DAYS_TO_ANALYSE"]["DAYS_IN_HOSPITAL"]),
expand("data/processed/{pid}/targets_{summarised}.csv", expand("data/processed/{pid}/targets_{summarised}.csv",
pid = config["PIDS"], pid = config["PIDS"],
summarised = config["PARAMS_FOR_ANALYSIS"]["SUMMARISED"]), summarised = config["PARAMS_FOR_ANALYSIS"]["SUMMARISED"]),