dada2.smk 428 Bytes
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DADA2    
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rule dada2:
	input:
		"work/filter/{sample}.fastq.gz"
	output:
		"work/dada/{sample}.rds"
	threads:
		config["THREADS"]
	script:
		"dada2.R"
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rule makeSequenceTable:
	input:
		expand("work/dada/{sample}.rds", sample=SAMPLES)
	output:
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		rds = "work/dada/seqtab.rds",
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		fasta = "work/dada/seqtab.fasta",
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		tsv = "work/dada/seqtab.tsv",
		biom = "work/dada/dada.biom"
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	threads:
		config["THREADS"]
	script:
		"makeSequenceTable.R"