global.smk 1.53 KB
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shell.executable("/bin/bash")
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shell.prefix("source ~/.bashrc; ")
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import os
configfile: "./config.json"

rule all:
	input:
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		"report/multiqc_report.html",
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		expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
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		#coassembly
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quast    
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		"report/quast_coassembly/report.html",
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		expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
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		expand("report/count-genes-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
		"report/diamond_nr_coassembly.tsv",
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		"report/diamond_swissprot_coassembly.tsv",
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		"report/contigs_coassembly-taxNames.tsv",
		"report/genes_coassembly-taxNames.tsv",
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metabat    
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		"work/metabat/coassembly.done",
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checkm    
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		"work/checkm/coassembly/lineage.ms",
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		#catalogue
		"report/quast_results/report.html",
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		expand("report/count-contigs-catalogue-{sample}.tsv", sample=config["SAMPLES"]),
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		"report/diamond_nr_catalogue.tsv",
		"report/contigs_catalogue-taxNames.tsv",
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		#add-on
		expand("work/addon/{sample}.small_contigs.taxNames.tsv", sample=config["SAMPLES"]),
		#expand("work/addon/catalogue.{sample}.unmapped.taxNames.tsv", sample=config["SAMPLES"]),
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		#virome
		"report/viromeQC.txt",
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include: "../workflow_metagenomics/quality.smk"
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include: "../workflow_metagenomics/preprocess.smk"
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include: "../workflow_metagenomics/kaiju.smk"
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khmer    
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include: "../workflow_metagenomics/assembly.smk"
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include: "../workflow_metagenomics/annotation.smk"
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include: "../workflow_metagenomics/count.smk"
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include: "../workflow_metagenomics/catalogue.smk"
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include: "../workflow_metagenomics/add-on.smk"
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include: "../workflow_metagenomics/virome.smk"