checkm

catalogue.smk

@@ -162,3 +162,25 @@ rule resume_metabat:
 		done = temp("work/metabat/{sample}.done")
 	shell:
 		"touch {output.done} "
+
+rule checkm:
+	input:
+		"work/metabat/{sample}/{sample}.unbinned.fa"
+	output:
+		"work/checkm/{sample}/checkm.log"
+	threads:
+		8
+	params:
+		input = lambda wildcards, input: os.path.dirname(str(input)),
+		output = lambda wildcards, output: os.path.dirname(str(output))
+	shell:
+		"conda activate checkm-genome-1.0.18 "
+		" ; "
+		"checkm "
+		"lineage_wf "
+		"-t {threads} "
+		"-x fa "
+		"{params.output} "
+		"{params.input} "
+		" ; "
+		"conda deactivate"