Move inputs to appropriate directive

Author: ahmig

workflow/rules/report.smk

@@ -98,12 +98,12 @@ rule general_NV_description:
     params:
         samples = expand("{sample}", sample = iter_samples()),
         design = config["PLOTS"],
-        regions = config["PLOT_GENOME_REGIONS"],
-        coordinates = config["COORDINATES_JSON"],
         window = config["WINDOW"]["WIDTH"],
         step = config["WINDOW"]["STEP"],
         max_alt_freq = 1.0 - config["VC"]["IVAR_FREQ"]
     input:
+        coordinates = config["COORDINATES_JSON"],
+        regions = config["PLOT_GENOME_REGIONS"],
         window = OUTDIR/f"{OUTPUT_NAME}.window.csv",
         vcf =  OUTDIR/f"{OUTPUT_NAME}.masked.filtered.tsv",
         metadata = config["METADATA"]

workflow/scripts/report/NV_description.R

@@ -118,7 +118,7 @@ vcf <- vcf %>%
   )
 
 # NSP data
-npc <- read_csv(snakemake@params[["regions"]]) %>%
+npc <- read_csv(snakemake@input[["regions"]]) %>%
   mutate(
     summary_nsp = case_when(
       region %in% paste("nsp", seq(4, 12, 1), sep = "") ~ "nsp4-12",