diff --git a/assembly.smk b/assembly.smk index bb03a030997eeeee404c842c08573e8eea2ea912..d359f42358f35befd36360118249bcb810e24a13 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 460dcdc3597e7f0d1f2cb5e3aac2f9c2099c22e0..dbb749cead309d1e01e9baaff9e319d5c46b3989 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"