metabat output .fa

catalogue.smk

@@ -127,7 +127,6 @@ checkpoint metabat:
 		"--minContig 5000 "
 		"--minClsSize {params.clustrsize} "
 		"--numThreads {threads} "
-		"--onlyLabel "
 		"--unbinned "
 		"--verbose "
 		" ; "
@@ -135,15 +134,19 @@ checkpoint metabat:
 
 rule metabat_kaiju:
 	input:
-		clustr = "work/metabat/{sample}/{sample}.{num}",
+		clustr = "work/metabat/{sample}/{sample}.{num}.fa",
 		kaiju = "report/contigs_{sample}-taxNames.tsv"
 	output:
 		"work/metabat/{sample}/{sample}.{num}_kaiju.tsv"
 	shell:
+		"grep "
+		"'>' "
+		"--file {input.clustr} "
+		" | "
 		"grep "
 		"--no-messages "
 		"--word-regexp "
-		"--file {input.clustr} "
+		"--file - "
 		"{input.kaiju} "
 		" > "
 		"{output} "