tree.nwk

affiliation.smk

@@ -55,7 +55,8 @@ rule tree:
 		biom = "work/FROGS/affiliation.biom"
 	output:
 		html = "work/FROGS/tree.html",
-		nwk = "work/FROGS/tree.nwk"
+		nwk = "work/FROGS/tree.nwk",
+		log = "work/FROGS/tree.log"
 	threads:
 		config["THREADS"]
 	shell:
@@ -63,10 +64,11 @@ rule tree:
 		"&& "
 		"tree.py "
 		"--nb-cpus {threads} "
-		"--input-sequences {input.fasta} "
-		"--biom-file {input.biom} "
-		"--html {output.html} "
+		"--input-otu {input.fasta} "
+		"--biomfile {input.biom} "
 		"--out-tree {output.nwk} "
+		"--html {output.html} "
+		"--log-file {output.log}"
 		"&& "
 		"conda deactivate"