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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