From 29e6c2572d2d16786de28949f9de449365a1e7bd Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Thu, 5 Sep 2019 11:48:49 +0200
Subject: [PATCH] quast
---
assembly.smk | 46 ++++++++++++++++++++++++++++++++++++++++++++++
global.smk | 1 +
2 files changed, 47 insertions(+)
diff --git a/assembly.smk b/assembly.smk
index bb03a03..d359f42 100644
--- a/assembly.smk
+++ b/assembly.smk
@@ -99,3 +99,49 @@ def contigs_input(wildcards):
return ["work/megahit/{wildcards.sample}/{wildcards.sample}.contigs.fa".format(wildcards=wildcards)]
elif config["ASSEMBLER"] == "metaspades":
return ["work/metaSPADES/{wildcards.sample}/{wildcards.sample}.contigs.fasta".format(wildcards=wildcards)]
+
+def contigsExpand_input(wildcards):
+ if config["ASSEMBLER"] == "megahit":
+ return [expand("work/megahit/{sample}/{sample}.contigs.fa", sample=SAMPLES)]
+ elif config["ASSEMBLER"] == "metaspades":
+ return [expand("work/metaSPADES/{sample}/{sample}.contigs.fasta", sample=SAMPLES)]
+
+def coassembly_contigs_input(wildcards):
+ if config["ASSEMBLER"] == "megahit":
+ return ["work/megahit/coassembly/coassembly.contigs.fa"]
+ elif config["ASSEMBLER"] == "metaspades":
+ return ["work/metaSPADES/coassembly/coassembly.contigs.fasta"]
+
+rule quast:
+ input:
+ unpack(contigsExpand_input)
+ output:
+ "report/quast_results/report.html"
+ threads:
+ 4
+ params:
+ output = lambda wildcards, output: os.path.dirname(str(output))
+ shell:
+ "quast "
+ "--mgm "
+ "--output-dir {params.output} "
+ "-L "
+ "--threads {threads} "
+ "{input} "
+
+rule coassembly_quast:
+ input:
+ unpack(coassembly_contigs_input)
+ output:
+ "report/quast_coassembly/report.html"
+ threads:
+ 4
+ params:
+ output = lambda wildcards, output: os.path.dirname(str(output))
+ shell:
+ "quast "
+ "--mgm "
+ "--output-dir {params.output} "
+ "-L "
+ "--threads {threads} "
+ "{input} "
diff --git a/global.smk b/global.smk
index 460dcdc..dbb749c 100644
--- a/global.smk
+++ b/global.smk
@@ -9,6 +9,7 @@ rule all:
"report/multiqc_report.html",
expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
"report/contigs_coassembly-taxNames.tsv",
+ "report/quast_coassembly/report.html",
include: "../workflow_metagenomics/quality.smk"
include: "../workflow_metagenomics/preprocess.smk"
--
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