From 3ac804285ab66dd31b064c085d69d72272842b3e Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Mon, 3 Feb 2020 14:35:12 +0100
Subject: [PATCH] checkm

---
 catalogue.smk | 6 +++---
 global.smk    | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/catalogue.smk b/catalogue.smk
index 61c1289..7e67aa5 100644
--- a/catalogue.smk
+++ b/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"
diff --git a/global.smk b/global.smk
index 68c0b4a..03b1de5 100644
--- a/global.smk
+++ b/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"]),
-- 
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