checkm

catalogue.smk

@@ -167,9 +167,9 @@ rule checkm:
 	input:
 		"work/metabat/{sample}/{sample}.unbinned.fa"
 	output:
-		"work/checkm/{sample}/checkm.log"
+		"work/checkm/{sample}/lineage.ms"
 	threads:
-		8
+		4
 	params:
 		input = lambda wildcards, input: os.path.dirname(str(input)),
 		output = lambda wildcards, output: os.path.dirname(str(output))
@@ -180,7 +180,7 @@ rule checkm:
 		"lineage_wf "
 		"-t {threads} "
 		"-x fa "
-		"{params.output} "
 		"{params.input} "
+		"{params.output} "
 		" ; "
 		"conda deactivate"

global.smk

@@ -17,6 +17,7 @@ rule all:
 		"report/contigs_coassembly-taxNames.tsv",
 		"report/genes_coassembly-taxNames.tsv",
 		"work/metabat/coassembly.done",
+		"work/checkm/coassembly/lineage.ms",
 		#catalogue
 		"report/quast_results/report.html",
 		expand("report/count-contigs-catalogue-{sample}.tsv", sample=config["SAMPLES"]),