catalogue debug

annotation.smk

@@ -41,7 +41,7 @@ rule prodigal:
 
 def faa_input(wildcards):
 	if wildcards.sample == "catalogue":
-		return ["work/cdhit/catalogue.faa"]
+		return {"faa": "work/cdhit/catalogue.faa"}
 	else :
 		if config["PROTEINS-PREDICTOR"] == "FragGeneScan":
 			return {"faa": "work/FGS/{wildcards.sample}/{wildcards.sample}_FGS.faa".format(wildcards=wildcards)}

catalogue.smk

@@ -83,10 +83,10 @@ rule cd_hit_2D:
 
 rule faa_catalogue:
 	input:
-		ffn = "work/cdhit/catalogue.ffn"
-		faa = expand("work/prodigal/{sample}/{sample}.faa", sample=config["SAMPLES"])
+		ffn = "work/cdhit/catalogue.ffn",
+		faa = expand("work/prodigal/{sample}/{sample}_prodigal.faa", sample=config["SAMPLES"])
 	output:
-		list = temp("work/cdhit/catalogue.list")
+		list = temp("work/cdhit/catalogue.list"),
 		faa = "work/cdhit/catalogue.faa"
 	threads:
 		2