From 49e505241338e14f94d1747b707add416e8d38c6 Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Mon, 3 Feb 2020 11:05:32 +0100
Subject: [PATCH] checkm
---
catalogue.smk | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/catalogue.smk b/catalogue.smk
index a52abe5..61c1289 100644
--- a/catalogue.smk
+++ b/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"
--
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