Exécution d'un workflow (snakemake)

module6/ressources/incidence_syndrome_grippal_snakemake/Snakefile

@@ -37,3 +37,12 @@ rule histogram:
         "data/annual-incidence-histogram.png"
      script:
         "scripts/annual-incidence-histogram.R"
+
+rule all:
+     input:
+        "data/weekly-incidence.csv",
+        "data/preprocessed-weekly-incidence.csv",
+        "data/weekly-incidence-plot.png",
+        "data/weekly-incidence-plot-last-years.png",
+        "data/annual-incidence.csv",
+        "data/annual-incidence-histogram.png"

module6/ressources/incidence_syndrome_grippal_snakemake/scripts/incidence-plots.R

 # Read in the data and convert the dates
 data = read.csv(snakemake@input[[1]])
-names(data) <- c("date", "incidence")
-data$date <- as.Date(data$date)
+data$week_starting <- as.Date(data$week_starting)
 
 # Plot the complete incidence dataset
 png(filename=snakemake@output[[1]])